1
|
Minnelli C, Mangiaterra G, Laudadio E, Citterio B, Rinaldi S. Investigation on the Synergy between Membrane Permeabilizing Amphiphilic α-Hydrazido Acids and Commonly Used Antibiotics against Drug-Resistant Bacteria. Molecules 2024; 29:4078. [PMID: 39274926 PMCID: PMC11397519 DOI: 10.3390/molecules29174078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Revised: 08/21/2024] [Accepted: 08/26/2024] [Indexed: 09/16/2024] Open
Abstract
The growth of (multi)drug resistance in bacteria is among the most urgent global health issues. Monocationic amphiphilic α-hydrazido acid derivatives are structurally simple mimics of antimicrobial peptides (AMPs) with fewer drawbacks. Their mechanism of membrane permeabilization at subtoxic concentrations was found to begin with an initial electrostatic attraction of isolated amphiphile molecules to the phospholipid heads, followed by a rapid insertion of the apolar portions. As the accumulation into the bilayer proceeded, the membrane increased its fluidity and permeability without being subjected to major structural damage. After having ascertained that α-hydrazido acid amphiphiles do not interact with bacterial DNA, they were subjected to synergy evaluation for combinations with conventional antibiotics. Synergy was observed for combinations with tetracycline against sensitive S. aureus and E. coli, as well as with ciprofloxacin and colistin against resistant strains. Additivity with a remarkable recovery in activity of conventional antibiotics (from 2-fold to ≥32-fold) together with largely subtoxic concentrations of α-hydrazido acid derivatives was found for combinations with ciprofloxacin toward susceptible S. aureus and methicillin toward MRSa. However, no potentiation of conventional antibiotics was observed for combinations with linezolid and gentamicin against the corresponding resistant S. aureus and E. coli strains.
Collapse
Affiliation(s)
- Cristina Minnelli
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Gianmarco Mangiaterra
- Department of Biomolecular Science, University of Urbino "Carlo Bo", 61032 Urbino, Italy
| | - Emiliano Laudadio
- Department of Science and Engineering of Matter, Environment and Urban Planning, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Barbara Citterio
- Department of Biomolecular Science, University of Urbino "Carlo Bo", 61032 Urbino, Italy
| | - Samuele Rinaldi
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| |
Collapse
|
2
|
Yamamoto S, Yamamoto K, Hirao Y, Yamaguchi K, Nakajima K, Sato M, Kawachi M, Domon M, Goto K, Omori K, Iino N, Shimada H, Aoyagi R, Ei I, Goto S, Goto Y, Gejyo F, Yamamoto T, Narita I. Mass spectrometry-based proteomic analysis of proteins adsorbed by hexadecyl-immobilized cellulose bead column for the treatment of dialysis-related amyloidosis. Amyloid 2024; 31:105-115. [PMID: 38343068 DOI: 10.1080/13506129.2024.2315148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 02/01/2024] [Indexed: 02/27/2024]
Abstract
BACKGROUND Dialysis-related amyloidosis (DRA) is a severe complication in end-stage kidney disease (ESKD) patients undergoing long-term dialysis treatment, characterized by the deposition of β2-microglobulin-related amyloids (Aβ2M amyloid). To inhibit DRA progression, hexadecyl-immobilized cellulose bead (HICB) columns are employed to adsorb circulating β2-microglobulin (β2M). However, it is possible that the HICB also adsorbs other molecules involved in amyloidogenesis. METHODS We enrolled 14 ESKD patients using HICB columns for DRA treatment; proteins were extracted from HICBs following treatment and identified using liquid chromatography-linked mass spectrometry. We measured the removal rate of these proteins and examined the effect of those molecules on Aβ2M amyloid fibril formation in vitro. RESULTS We identified 200 proteins adsorbed by HICBs. Of these, 21 were also detected in the amyloid deposits in the carpal tunnels of patients with DRA. After passing through the HICB column and hemodialyzer, the serum levels of proteins such as β2M, lysozyme, angiogenin, complement factor D and matrix Gla protein were reduced. These proteins acted in the Aβ2M amyloid fibril formation. CONCLUSIONS HICBs adsorbed diverse proteins in ESKD patients with DRA, including those detected in amyloid lesions. Direct hemoperfusion utilizing HICBs may play a role in acting Aβ2M amyloidogenesis by reducing the amyloid-related proteins.
Collapse
Affiliation(s)
- Suguru Yamamoto
- Division of Clinical Nephrology and Rheumatology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Keiko Yamamoto
- Biofluid Biomarker Center, Niigata University, Niigata, Japan
| | - Yoshitoshi Hirao
- Instrumental Analysis Section, Okinawa Institute of Science and Technology, Onna, Japan
| | | | | | - Mami Sato
- Sakelogy Center, Niigata University, Niigata, Japan
| | - Miho Kawachi
- Division of Clinical Chemistry, Niigata University Graduate School of Health Sciences, Niigata, Japan
| | - Mio Domon
- Division of Clinical Nephrology and Rheumatology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Kei Goto
- Division of Nephrology, Agano Municipal Hospital, Niigata, Japan
| | | | - Noriaki Iino
- Division of Nephrology, Uonuma Kikan Hospital, Niigata, Japan
| | | | - Ryuzi Aoyagi
- Department of Nephrology, Tachikawa General Hospital, Niigata, Japan
| | - Isei Ei
- Santo-Second Clinic, Niigata, Japan
| | - Shin Goto
- Division of Clinical Nephrology and Rheumatology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Yuji Goto
- Graduate School of Engineering, Osaka University, Osaka, Japan
| | - Fumitake Gejyo
- Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
| | - Tadashi Yamamoto
- Biofluid Biomarker Center, Niigata University, Niigata, Japan
- Department of Clinical Laboratory, Shinrakuen Hospital, Niigata, Japan
| | - Ichiei Narita
- Division of Clinical Nephrology and Rheumatology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| |
Collapse
|
3
|
Bulyáki É, Kun J, Molnár T, Papp A, Micsonai A, Vadászi H, Márialigeti B, Kovács AI, Gellén G, Yamaguchi K, Lin Y, So M, Józsi M, Schlosser G, Lee YH, Liliom K, Goto Y, Kardos J. Pathogenic D76N Variant of β 2-Microglobulin: Synergy of Diverse Effects in Both the Native and Amyloid States. BIOLOGY 2021; 10:biology10111197. [PMID: 34827190 PMCID: PMC8614874 DOI: 10.3390/biology10111197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/11/2021] [Accepted: 11/11/2021] [Indexed: 01/13/2023]
Abstract
Simple Summary Elevated β2-microglobulin (β2m) serum levels cause serious complications in patients on long-term kidney dialysis by depositing in the form of amyloid fibrils in the osteoarticular system. Recently, a hereditary systemic amyloidosis was discovered, caused by a naturally occurring D76N β2m mutant exhibiting normal serum levels and a distinct, visceral deposition pattern. D76N β2m showed a structure remarkably similar to the wild-type (WT) protein, albeit with decreased thermodynamic stability and increased amyloidogenicity. Despite the extensive research, the molecular bases of the aberrant aggregation of β2m in vivo remains elusive. Here, using a variety of biophysical techniques, we investigated the role of the pathogenic D76N mutation in the amyloid formation of β2m by point mutations affecting the stabilizing ion-pairs of β2m. We found that, relative to WT β2m, the exceptional amyloidogenicity of the pathogenic D76N β2m variant is realized by the synergy of diverse effects of destabilized native structure, higher sensitivity to negatively charged amphiphilic molecules and polyphosphate, more effective fibril nucleation, higher conformational stability of fibrils, and elevated affinity for extracellular matrix proteins. Understanding the underlying molecular mechanisms might help to find target points for effective treatments against diseases associated with the deleterious aggregation of proteins. Abstract β2-microglobulin (β2m), the light chain of the MHC-I complex, is associated with dialysis-related amyloidosis (DRA). Recently, a hereditary systemic amyloidosis was discovered, caused by a naturally occurring D76N β2m variant, which showed a structure remarkably similar to the wild-type (WT) protein, albeit with decreased thermodynamic stability and increased amyloidogenicity. Here, we investigated the role of the D76N mutation in the amyloid formation of β2m by point mutations affecting the Asp76-Lys41 ion-pair of WT β2m and the charge cluster on Asp38. Using a variety of biophysical techniques, we investigated the conformational stability and partial unfolding of the native state of the variants, as well as their amyloidogenic propensity and the stability of amyloid fibrils under various conditions. Furthermore, we studied the intermolecular interactions of WT and mutant proteins with various binding partners that might have in vivo relevance. We found that, relative to WT β2m, the exceptional amyloidogenicity of the pathogenic D76N β2m variant is realized by the deleterious synergy of diverse effects of destabilized native structure, higher sensitivity to negatively charged amphiphilic molecules (e.g., lipids) and polyphosphate, more effective fibril nucleation, higher conformational stability of fibrils, and elevated affinity for extracellular components, including extracellular matrix proteins.
Collapse
Affiliation(s)
- Éva Bulyáki
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary; (É.B.); (J.K.); (A.M.); (H.V.)
| | - Judit Kun
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary; (É.B.); (J.K.); (A.M.); (H.V.)
| | - Tamás Molnár
- Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary; (T.M.); (B.M.); (A.I.K.)
| | - Alexandra Papp
- Complement Research Group, Department of Immunology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary; (A.P.); (M.J.)
| | - András Micsonai
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary; (É.B.); (J.K.); (A.M.); (H.V.)
| | - Henrietta Vadászi
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary; (É.B.); (J.K.); (A.M.); (H.V.)
| | - Borbála Márialigeti
- Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary; (T.M.); (B.M.); (A.I.K.)
| | - Attila István Kovács
- Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary; (T.M.); (B.M.); (A.I.K.)
| | - Gabriella Gellén
- Department of Analytical Chemistry, Institute of Chemistry, ELTE Eötvös Loránd University, 1117 Budapest, Hungary; (G.G.); (G.S.)
| | - Keiichi Yamaguchi
- Global Center for Medical Engineering and Informatics, Osaka University, Osaka 565-0871, Japan; (K.Y.); (Y.G.)
| | - Yuxi Lin
- Research Center of Bioconvergence Analysis, Korea Basic Science Institute (KBSI), Ochang 28119, Korea; (Y.L.); (Y.-H.L.)
| | - Masatomo So
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan; or
| | - Mihály Józsi
- Complement Research Group, Department of Immunology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary; (A.P.); (M.J.)
- MTA-ELTE Complement Research Group, Eötvös Loránd Research Network (ELKH), Department of Immunology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary
| | - Gitta Schlosser
- Department of Analytical Chemistry, Institute of Chemistry, ELTE Eötvös Loránd University, 1117 Budapest, Hungary; (G.G.); (G.S.)
| | - Young-Ho Lee
- Research Center of Bioconvergence Analysis, Korea Basic Science Institute (KBSI), Ochang 28119, Korea; (Y.L.); (Y.-H.L.)
- Bio-Analytical Science, University of Science and Technology (UST), Daejeon 34113, Korea
- Graduate School of Analytical Science and Technology (GRAST), Chungnam National University (CNU), Daejeon 34134, Korea
- Research Headquarters, Korea Brain Research Institute (KBRI), Daegu 41068, Korea
| | - Károly Liliom
- Department of Biophysics and Radiation Biology, Faculty of Medicine, Semmelweis University, 1094 Budapest, Hungary;
| | - Yuji Goto
- Global Center for Medical Engineering and Informatics, Osaka University, Osaka 565-0871, Japan; (K.Y.); (Y.G.)
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan; or
| | - József Kardos
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary; (É.B.); (J.K.); (A.M.); (H.V.)
- Correspondence:
| |
Collapse
|
4
|
J S Loureiro R, Vila-Viçosa D, Machuqueiro M, Shakhnovich EI, F N Faísca P. The Early Phase of β2m Aggregation: An Integrative Computational Study Framed on the D76N Mutant and the ΔN6 Variant. Biomolecules 2019; 9:biom9080366. [PMID: 31416179 PMCID: PMC6722664 DOI: 10.3390/biom9080366] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 08/08/2019] [Accepted: 08/13/2019] [Indexed: 12/12/2022] Open
Abstract
Human β2-microglobulin (b2m) protein is classically associated with dialysis-related amyloidosis (DRA). Recently, the single point mutant D76N was identified as the causative agent of a hereditary systemic amyloidosis affecting visceral organs. To get insight into the early stage of the β2m aggregation mechanism, we used molecular simulations to perform an in depth comparative analysis of the dimerization phase of the D76N mutant and the ΔN6 variant, a cleaved form lacking the first six N-terminal residues, which is a major component of ex vivo amyloid plaques from DRA patients. We also provide first glimpses into the tetramerization phase of D76N at physiological pH. Results from extensive protein–protein docking simulations predict an essential role of the C- and N-terminal regions (both variants), as well as of the BC-loop (ΔN6 variant), DE-loop (both variants) and EF-loop (D76N mutant) in dimerization. The terminal regions are more relevant under acidic conditions while the BC-, DE- and EF-loops gain importance at physiological pH. Our results recapitulate experimental evidence according to which Tyr10 (A-strand), Phe30 and His31 (BC-loop), Trp60 and Phe62 (DE-loop) and Arg97 (C-terminus) act as dimerization hot-spots, and further predict the occurrence of novel residues with the ability to nucleate dimerization, namely Lys-75 (EF-loop) and Trp-95 (C-terminus). We propose that D76N tetramerization is mainly driven by the self-association of dimers via the N-terminus and DE-loop, and identify Arg3 (N-terminus), Tyr10, Phe56 (D-strand) and Trp60 as potential tetramerization hot-spots.
Collapse
Affiliation(s)
- Rui J S Loureiro
- BioISI-Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Diogo Vila-Viçosa
- BioISI-Biosystems & Integrative Sciences Institute and Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Miguel Machuqueiro
- BioISI-Biosystems & Integrative Sciences Institute and Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Eugene I Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Patrícia F N Faísca
- BioISI-Biosystems & Integrative Sciences Institute and Departamento de Física, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal.
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Yamamoto S. Molecular mechanisms underlying uremic toxin-related systemic disorders in chronic kidney disease: focused on β 2-microglobulin-related amyloidosis and indoxyl sulfate-induced atherosclerosis-Oshima Award Address 2016. Clin Exp Nephrol 2018; 23:151-157. [PMID: 29869756 PMCID: PMC6510801 DOI: 10.1007/s10157-018-1588-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Accepted: 05/07/2018] [Indexed: 11/27/2022]
Abstract
Uremic toxins are linked to chronic kidney disease (CKD)-related systemic diseases. β2-Microglobulin (β2-m), a water-soluble, middle-sized molecule, is associated with mortality and dialysis-related amyloidosis (DRA). DRA occurs in long-term dialysis patients, with β2-m amyloid deposited mainly in osteoarticular tissues. We investigated a model of β2-m amyloid fibril extension at neutral pH in the presence of trifluoroethanol or sodium dodecyl sulfate. Using this model, some biological molecules, including glycosaminoglycans and lysophospholipids, were found to be chaperones for β2-m amyloid fibril extension. Several protein-bound solutes, such as indoxyl sulfate (IS) and p-cresyl sulfate, are independent risk factors for cardiovascular disease in CKD patients, especially those undergoing dialysis. We investigated kidney injury-induced acceleration of atherosclerosis in association with macrophage phenotypic change to a proinflammatory state as well as increased IS deposition in lesions in an animal model. IS directly induced macrophage inflammation and impaired cholesterol efflux to high-density lipoprotein (HDL) in vitro. In addition, a clinical study showed that HDL isolated from CKD patients induced proinflammatory reactions and impaired cholesterol efflux to macrophages. These findings suggest that protein-bound solutes, including IS, will induce dysfunction of both macrophages and HDL in atherosclerotic lesions. To remove uremic toxins efficiently, we demonstrated the potential efficacy of oral charcoal adsorbent and hexadecyl-immobilized cellulose beads in hemodialysis patients. These findings suggest that uremic toxins induce various CKD-related systemic disorders, and further therapeutic strategies will be needed to reduce uremic toxins enough and improve life expectancy in CKD patients.
Collapse
Affiliation(s)
- Suguru Yamamoto
- Division of Clinical Nephrology and Rheumatology, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Niigata, 951-8510, Japan.
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Naiki H, Okoshi T, Ozawa D, Yamaguchi I, Hasegawa K. Molecular pathogenesis of human amyloidosis: Lessons from β2 -microglobulin-related amyloidosis. Pathol Int 2016; 66:193-201. [PMID: 26969800 DOI: 10.1111/pin.12394] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 01/28/2016] [Accepted: 01/29/2016] [Indexed: 01/02/2023]
Abstract
Amyloidosis refers to a group of diseases with amyloid fibrils deposited in various organs and is classified into more than 30 diseases in humans based on the kind of amyloid protein. In order to elucidate the molecular pathogenesis of human amyloidosis, we studied the molecular mechanism of amyloid fibril formation in vitro. We first developed a novel fluorometric method to determine amyloid fibrils in vitro based on the unique characteristics of thioflavin T. We next proposed a nucleation-dependent polymerization model to explain the general mechanism of amyloid fibril formation in vitro. Based on this model, we characterized the biological molecular interactions that promote or inhibit amyloid fibril formation in vitro and developed models of pathological molecular environment for inducing human β2-microglobulin-related amyloidosis in long-term hemodialysis patients. We also proposed a novel and attractive cytotoxic mechanism of β2-microglobulin amyloid fibrils, that is, the disruption of endosomal/lysosomal membranes by endocytosed amyloid fibrils. These findings may be useful to elucidate the molecular pathogenesis of other kinds of human amyloidosis.
Collapse
Affiliation(s)
- Hironobu Naiki
- Department of Pathological Sciences, Faculty of Medical Sciences, University of Fukui, Fukui, Japan
| | - Tadakazu Okoshi
- Department of Pathological Sciences, Faculty of Medical Sciences, University of Fukui, Fukui, Japan
| | - Daisaku Ozawa
- Department of Pathological Sciences, Faculty of Medical Sciences, University of Fukui, Fukui, Japan
| | - Itaru Yamaguchi
- Department of Pathological Sciences, Faculty of Medical Sciences, University of Fukui, Fukui, Japan
| | - Kazuhiro Hasegawa
- Department of Pathological Sciences, Faculty of Medical Sciences, University of Fukui, Fukui, Japan
| |
Collapse
|
9
|
Chaturvedi SK, Khan JM, Siddiqi MK, Alam P, Khan RH. Comparative insight into surfactants mediated amyloidogenesis of lysozyme. Int J Biol Macromol 2016; 83:315-25. [DOI: 10.1016/j.ijbiomac.2015.11.053] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 11/18/2015] [Accepted: 11/19/2015] [Indexed: 12/14/2022]
|
10
|
Khan JM, Khan MS, Ali MS, Al-Shabib NA, Khan RH. Cetyltrimethylammonium bromide (CTAB) promote amyloid fibril formation in carbohydrate binding protein (concanavalin A) at physiological pH. RSC Adv 2016. [DOI: 10.1039/c6ra03707k] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Low concentration of CTAB provoked cross β-sheet formation whereas high concentrations of CTAB direct to alpha helix induction in Con A.
Collapse
Affiliation(s)
- Javed Masood Khan
- Department of Food Science and Nutrition
- Faculty of Food and Agricultural Sciences
- King Saud University
- 2460 Riyadh 11451
- Saudi Arabia
| | - Mohd Shahnawaz Khan
- Protein Research Chair
- Department of Biochemistry
- College of Science
- King Saud University
- Riyadh
| | - Mohd Sajid Ali
- Department of Chemistry
- King Saud University
- Riyadh 11451
- Saudi Arabia
| | - Nasser Abdulatif Al-Shabib
- Department of Food Science and Nutrition
- Faculty of Food and Agricultural Sciences
- King Saud University
- 2460 Riyadh 11451
- Saudi Arabia
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit
- Aligarh Muslim University
- Aligarh
- India
| |
Collapse
|
11
|
Cournia Z, Allen TW, Andricioaei I, Antonny B, Baum D, Brannigan G, Buchete NV, Deckman JT, Delemotte L, del Val C, Friedman R, Gkeka P, Hege HC, Hénin J, Kasimova MA, Kolocouris A, Klein ML, Khalid S, Lemieux MJ, Lindow N, Roy M, Selent J, Tarek M, Tofoleanu F, Vanni S, Urban S, Wales DJ, Smith JC, Bondar AN. Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory. J Membr Biol 2015; 248:611-40. [PMID: 26063070 PMCID: PMC4515176 DOI: 10.1007/s00232-015-9802-0] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 03/26/2015] [Indexed: 01/05/2023]
Abstract
Membrane proteins mediate processes that are fundamental for the flourishing of biological cells. Membrane-embedded transporters move ions and larger solutes across membranes; receptors mediate communication between the cell and its environment and membrane-embedded enzymes catalyze chemical reactions. Understanding these mechanisms of action requires knowledge of how the proteins couple to their fluid, hydrated lipid membrane environment. We present here current studies in computational and experimental membrane protein biophysics, and show how they address outstanding challenges in understanding the complex environmental effects on the structure, function, and dynamics of membrane proteins.
Collapse
Affiliation(s)
- Zoe Cournia
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527, Athens, Greece
| | - Toby W. Allen
- School of Applied Sciences & Health Innovations Research Institute, RMIT University, GPO Box 2476, Melbourne, Vic, 3001, Australia; and Department of Chemistry, University of California, Davis. Davis, CA 95616, USA
| | - Ioan Andricioaei
- Department of Chemistry, University of California, Irvine, CA 92697
| | - Bruno Antonny
- Institut de Pharmacologie Moléculaire et Cellulaire, Université de Nice Sophia-Antipolis and Centre National de la Recherche Scientifique, UMR 7275, 06560 Valbonne, France
| | - Daniel Baum
- Department of Visualization and Data Analysis, Zuse Institute Berlin, Takustrasse 7, D-14195 Berlin, Germany
| | - Grace Brannigan
- Center for Computational and Integrative Biology and Department of Physics, Rutgers University-Camden, Camden, NJ, USA
| | - Nicolae-Viorel Buchete
- School of Physics and Complex and Adaptive Systems Laboratory, University College Dublin, Belfield, Dublin 4, Ireland
| | | | - Lucie Delemotte
- Institute of Computational and Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Coral del Val
- Department of Artificial Intelligence, University of Granada, E-18071 Granada, Spain
| | - Ran Friedman
- Linnæus University, Department of Chemistry and Biomedical Sciences & Centre for Biomaterials Chemistry, 391 82 Kalmar, Sweden
| | - Paraskevi Gkeka
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527, Athens, Greece
| | - Hans-Christian Hege
- Department of Visualization and Data Analysis, Zuse Institute Berlin, Takustrasse 7, D-14195 Berlin, Germany
| | - Jérôme Hénin
- Laboratoire de Biochimie Théorique, IBPC and CNRS, Paris, France
| | - Marina A. Kasimova
- Université de Lorraine, SRSMC, UMR 7565, Vandoeuvre-lès-Nancy, F-54500, France
- Lomonosov Moscow State University, Moscow, 119991, Russian Federation
| | - Antonios Kolocouris
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Athens, Panepistimioupolis-Zografou, 15771 Athens, Greece
| | - Michael L. Klein
- Institute of Computational and Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Syma Khalid
- Department of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, UK
| | - M. Joanne Lemieux
- Department of Biochemistry, Faculty of Medicine & Dentistry, Membrane Protein Disease Research Group, and Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2H7
| | - Norbert Lindow
- Department of Visualization and Data Analysis, Zuse Institute Berlin, Takustrasse 7, D-14195 Berlin, Germany
| | - Mahua Roy
- Department of Chemistry, University of California, Irvine
| | - Jana Selent
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, IMIM (Hospital del Mar Medical Research Institute), Dr. Aiguader 88, E-08003 Barcelona, Spain
| | - Mounir Tarek
- Université de Lorraine, SRSMC, UMR 7565, Vandoeuvre-lès-Nancy, F-54500, France
- CNRS, SRSMC, UMR 7565, Vandoeuvre-lès-Nancy, F-54500, France
| | - Florentina Tofoleanu
- School of Physics and Complex and Adaptive Systems Laboratory, University College Dublin, Belfield, Dublin 4, Ireland
| | - Stefano Vanni
- Institut de Pharmacologie Moléculaire et Cellulaire, Université de Nice Sophia-Antipolis and Centre National de la Recherche Scientifique, UMR 7275, 06560 Valbonne, France
| | - Sinisa Urban
- Johns Hopkins University School of Medicine, Howard Hughes Medical Institute, Department of Molecular Biology & Genetics, 725 N. Wolfe Street, 507 Preclinical Teaching Building, Baltimore, MD 21205, USA
| | - David J. Wales
- University Chemical Laboratories, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Jeremy C. Smith
- Oak Ridge National Laboratory, PO BOX 2008 MS6309, Oak Ridge, TN 37831-6309, USA
| | - Ana-Nicoleta Bondar
- Theoretical Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
| |
Collapse
|
12
|
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.
Collapse
Affiliation(s)
- Vladimir Torbeev
- Laboratory of Organic Chemistry and ‡Laboratory of Physical Chemistry, ETH Zurich , Zurich CH-8093, Switzerland
| | | | | | | |
Collapse
|
13
|
Clingman CC, Deveau LM, Hay SA, Genga RM, Shandilya SMD, Massi F, Ryder SP. Allosteric inhibition of a stem cell RNA-binding protein by an intermediary metabolite. eLife 2014; 3. [PMID: 24935936 PMCID: PMC4094780 DOI: 10.7554/elife.02848] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 06/15/2014] [Indexed: 01/22/2023] Open
Abstract
Gene expression and metabolism are coupled at numerous levels. Cells must sense and respond to nutrients in their environment, and specialized cells must synthesize metabolic products required for their function. Pluripotent stem cells have the ability to differentiate into a wide variety of specialized cells. How metabolic state contributes to stem cell differentiation is not understood. In this study, we show that RNA-binding by the stem cell translation regulator Musashi-1 (MSI1) is allosterically inhibited by 18-22 carbon ω-9 monounsaturated fatty acids. The fatty acid binds to the N-terminal RNA Recognition Motif (RRM) and induces a conformational change that prevents RNA association. Musashi proteins are critical for development of the brain, blood, and epithelium. We identify stearoyl-CoA desaturase-1 as a MSI1 target, revealing a feedback loop between ω-9 fatty acid biosynthesis and MSI1 activity. We propose that other RRM proteins could act as metabolite sensors to couple gene expression changes to physiological state.
Collapse
Affiliation(s)
- Carina C Clingman
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Laura M Deveau
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Samantha A Hay
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Ryan M Genga
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Shivender M D Shandilya
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Francesca Massi
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Sean P Ryder
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| |
Collapse
|
14
|
Kumar S, Sharma P, Arora K, Raje M, Guptasarma P. Calcium binding to beta-2-microglobulin at physiological pH drives the occurrence of conformational changes which cause the protein to precipitate into amorphous forms that subsequently transform into amyloid aggregates. PLoS One 2014; 9:e95725. [PMID: 24755626 PMCID: PMC3995793 DOI: 10.1371/journal.pone.0095725] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 03/30/2014] [Indexed: 11/17/2022] Open
Abstract
Using spectroscopic, calorimetric and microscopic methods, we demonstrate that calcium binds to beta-2-microglobulin (β2m) under physiological conditions of pH and ionic strength, in biological buffers, causing a conformational change associated with the binding of up to four calcium atoms per β2m molecule, with a marked transformation of some random coil structure into beta sheet structure, and culminating in the aggregation of the protein at physiological (serum) concentrations of calcium and β2m. We draw attention to the fact that the sequence of β2m contains several potential calcium-binding motifs of the DXD and DXDXD (or DXEXD) varieties. We establish (a) that the microscopic aggregation seen at physiological concentrations of β2m and calcium turns into actual turbidity and visible precipitation at higher concentrations of protein and β2m, (b) that this initial aggregation/precipitation leads to the formation of amorphous aggregates, (c) that the formation of the amorphous aggregates can be partially reversed through the addition of the divalent ion chelating agent, EDTA, and (d) that upon incubation for a few weeks, the amorphous aggregates appear to support the formation of amyloid aggregates that bind to the dye, thioflavin T (ThT), resulting in increase in the dye's fluorescence. We speculate that β2m exists in the form of microscopic aggregates in vivo and that these don't progress to form larger amyloid aggregates because protein concentrations remain low under normal conditions of kidney function and β2m degradation. However, when kidney function is compromised and especially when dialysis is performed, β2m concentrations probably transiently rise to yield large aggregates that deposit in bone joints and transform into amyloids during dialysis related amyloidosis.
Collapse
Affiliation(s)
- Sukhdeep Kumar
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab, India
| | - Prerna Sharma
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab, India; Council of Scientific and Industrial Research, Institute of Microbial Technology (CSIR-IMTECH), Chandigarh, India
| | - Kanika Arora
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab, India
| | - Manoj Raje
- Council of Scientific and Industrial Research, Institute of Microbial Technology (CSIR-IMTECH), Chandigarh, India
| | - Purnananda Guptasarma
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab, India
| |
Collapse
|
15
|
Sultan A, Raman B, Rao CM, Tangirala R. The extracellular chaperone haptoglobin prevents serum fatty acid-promoted amyloid fibril formation of β2-microglobulin, resistance to lysosomal degradation, and cytotoxicity. J Biol Chem 2013; 288:32326-32342. [PMID: 24078632 DOI: 10.1074/jbc.m113.498337] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Fibril formation of β2-microglobulin and associated inflammation occur in patients on long term dialysis. We show that the plasma protein haptoglobin prevents the fatty acid-promoted de novo fibril formation of β2-microglobulin even at substoichiometric concentration. The fibrils are cytotoxic, and haptoglobin abolishes the cytotoxicity by preventing fibril formation. Haptoglobin does not alleviate the cytotoxicity of preformed fibrils. Fibrillar β2-microglobulin is resistant to lysosomal degradation. However, the species of β2-microglobulin populated in the presence of haptoglobin is susceptible to degradation. We observed that haptoglobin interacts with oligomeric prefibrillar species of β2-microglobulin but not with monomeric or fibrillar β2-microglobulin that may underlie the molecular mechanism. 1,1'-Bis(4-anilino)naphthalene-5,5'-disulfonic acid cross-linking to haptoglobin significantly compromises its chaperone activity, suggesting the involvement of hydrophobic surfaces. Haptoglobin is an acute phase protein whose level increases severalfold during inflammation, where local acidosis can occur. Our data show that haptoglobin prevents fibril formation of β2-microglobulin under conditions of physiological acidosis (between pH 5.5 and 6.5) but with relatively decreased efficiency. However, compromise in its chaperone activity under these conditions is more than compensated by its increased level of expression under inflammation. Erythrolysis is known to release hemoglobin into the plasma. Haptoglobin forms a 1:1 (mol/mol) complex with hemoglobin. This complex, like haptoglobin, interacts with the prefibrillar species of β2-microglobulin, preventing its fibril formation and the associated cytotoxicity and resistance to intracellular degradation. Thus, our study demonstrates that haptoglobin is a potential extracellular chaperone for β2-microglobulin even in moderately acidic conditions relevant during inflammation, with promising therapeutic implications in β2-microglobulin amyloid-related diseases.
Collapse
Affiliation(s)
- Abdullah Sultan
- From the Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology, Hyderabad 500 007, India
| | - Bakthisaran Raman
- From the Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology, Hyderabad 500 007, India
| | - Ch Mohan Rao
- From the Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology, Hyderabad 500 007, India.
| | - Ramakrishna Tangirala
- From the Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology, Hyderabad 500 007, India.
| |
Collapse
|
16
|
Fabian H, Gast K, Laue M, Jetzschmann KJ, Naumann D, Ziegler A, Uchanska-Ziegler B. IR spectroscopic analyses of amyloid fibril formation of β2-microglobulin using a simplified procedure for its in vitro generation at neutral pH. Biophys Chem 2013; 179:35-46. [PMID: 23727989 DOI: 10.1016/j.bpc.2013.05.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 04/29/2013] [Accepted: 05/01/2013] [Indexed: 11/16/2022]
Abstract
β2-microglobulin (β2m) is known to be the major component of fibrillar deposits in the joints of patients suffering from dialysis-related amyloidosis. We have developed a simplified procedure to convert monomeric recombinant β2m into amyloid fibrils at physiological pH by a combination of stirring and heating, enabling us to follow conformational changes associated with the assembly by infrared spectroscopy and electron microscopy. Our studies reveal that fibrillogenesis begins with the formation of relatively large aggregates, with secondary structure not significantly altered by the stirring-induced association. In contrast, the conversion of the amorphous aggregates into amyloid fibrils is associated with a profound re-organization at the level of the secondary and tertiary structures, leading to non-native like parallel arrangements of the β-strands in the fully formed amyloid structure of β2m. This study highlights the power of an approach to investigate the formation of β2m fibrils by a combination of biophysical techniques including IR spectroscopy.
Collapse
Affiliation(s)
- Heinz Fabian
- Robert Koch-Institut, ZBS 6, Nordufer 20, D-13353 Berlin, Germany.
| | | | | | | | | | | | | |
Collapse
|
17
|
Robal T, Larsson M, Martin M, Olivecrona G, Lookene A. Fatty acids bind tightly to the N-terminal domain of angiopoietin-like protein 4 and modulate its interaction with lipoprotein lipase. J Biol Chem 2012; 287:29739-52. [PMID: 22773878 DOI: 10.1074/jbc.m111.303529] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Angiopoietin-like protein 4 (Angptl4), a potent regulator of plasma triglyceride metabolism, binds to lipoprotein lipase (LPL) through its N-terminal coiled-coil domain (ccd-Angptl4) inducing dissociation of the dimeric enzyme to inactive monomers. In this study, we demonstrate that fatty acids reduce the inactivation of LPL by Angptl4. This was the case both with ccd-Angptl4 and full-length Angptl4, and the effect was seen in human plasma or in the presence of albumin. The effect decreased in the sequence oleic acid > palmitic acid > myristic acid > linoleic acid > linolenic acid. Surface plasmon resonance, isothermal titration calorimetry, fluorescence, and chromatography measurements revealed that fatty acids bind with high affinity to ccd-Angptl4. The interactions were characterized by fast association and slow dissociation rates, indicating formation of stable complexes. The highest affinity for ccd-Angptl4 was detected for oleic acid with a subnanomolar equilibrium dissociation constant (K(d)). The K(d) values for palmitic and myristic acid were in the nanomolar range. Linoleic and linolenic acid bound with much lower affinity. On binding of fatty acids, ccd-Angptl4 underwent conformational changes resulting in a decreased helical content, weakened structural stability, dissociation of oligomers, and altered fluorescence properties of the Trp-38 residue that is located close to the putative LPL-binding region. Based on these results, we propose that fatty acids play an important role in modulating the effects of Angptl4.
Collapse
Affiliation(s)
- Terje Robal
- Department of Chemistry, Tallinn University of Technology, Tallinn 12618, Estonia
| | | | | | | | | |
Collapse
|
18
|
Invernizzi G, Papaleo E, Sabate R, Ventura S. Protein aggregation: mechanisms and functional consequences. Int J Biochem Cell Biol 2012; 44:1541-54. [PMID: 22713792 DOI: 10.1016/j.biocel.2012.05.023] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Revised: 05/09/2012] [Accepted: 05/27/2012] [Indexed: 12/31/2022]
Abstract
Understanding the mechanisms underlying protein misfolding and aggregation has become a central issue in biology and medicine. Compelling evidence show that the formation of amyloid aggregates has a negative impact in cell function and is behind the most prevalent human degenerative disorders, including Alzheimer's Parkinson's and Huntington's diseases or type 2 diabetes. Surprisingly, the same type of macromolecular assembly is used for specialized functions by different organisms, from bacteria to human. Here we address the conformational properties of these aggregates, their formation pathways, their role in human diseases, their functional properties and how bioinformatics tools might be of help to study these protein assemblies.
Collapse
Affiliation(s)
- Gaetano Invernizzi
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | | | | | | |
Collapse
|
19
|
Abstract
Dialysis-related amyloidosis (DRA) is a clinical syndrome of pain, loss of function and other symptoms due to the deposition of amyloid consisting of β(2)-microglobulin (β(2)m) in the musculoskeletal system. The condition is seen in patients who suffer from chronic kidney disease and are treated with hemodialysis for a long time. Even though β(2)m easily can be manipulated to form amyloid in laboratory experiments under non-physiological conditions the precise mechanisms involved in the formation of β(2)m-amyloid in patients with DRA have been difficult to unravel. The current knowledge which is reviewed here indicates that conformational fluctuations centered around the D-strand, the DE-loop, and around the cis-configured Pro32 peptide bond are involved in β(2)m amyloidosis. Also required are highly increased concentrations of circulating β(2)m and possibly various post-translational modifications mediated by the pro-inflammatory environment in uremic blood, together with the influence of divalent metal ions (specifically Cu(2 +)), uremic toxins, and dialysis-enhanced redox-processes. It seems plausible that domain-swapped β(2)m dimers act as building blocks of β-spine cross-β -sheet fibrils consisting of otherwise globular, roughly natively folded protein. An activated complement system and cellular activation perpetuate these reactions which due to the affinity of β(2)m-amyloid for the collagen of synovial surfaces result in the DRA syndrome.
Collapse
Affiliation(s)
- Dorthe B Corlin
- Department of Clinical Biochemistry and Immunology, Division of Microbiology and Diagnostics, Statens Serum Institut, Bldg. 85/240, Artillerivej 5, 2300, Copenhagen S, Denmark,
| | | |
Collapse
|
20
|
Esposito G, Corazza A, Bellotti V. Pathological self-aggregation of β(2)-microglobulin: a challenge for protein biophysics. Subcell Biochem 2012; 65:165-183. [PMID: 23225003 DOI: 10.1007/978-94-007-5416-4_7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The pathological aggregation of b(2)-microglobulin (b2m) is examined starting from the relevance of some structural aspects of the protein. The systemic deposition of b2m fibrils has been ascribed to several factors, but no conclusive evidence emerged so far. The characterization of b2m aggregates by direct investigation through electron microscopy, atomic force microscopy, solid state NMR and other solid state techniques provides important structural and morphological information on the assembly, but no clues about the mechanism of the aggregation process. The most relevant mechanistic hypotheses are critically reviewed. In addition to the mechanisms exclusively based on structural features, also the recently reported prion-like conversion is analyzed and shown to hardly comply with some established conditions of the fibrillogenic process. An alternative mechanism is recalled that does not require rare events and involves only the full-length protein in proximity of collagen, i.e. the environment that physiologically supports deposition.
Collapse
Affiliation(s)
- Gennaro Esposito
- Dipartimento di Scienze Mediche e Biologiche, Università di Udine, P.le Kolbe, 4, 33100, Udine, Italy,
| | | | | |
Collapse
|
21
|
Friedman R, Caflisch A. Surfactant effects on amyloid aggregation kinetics. J Mol Biol 2011; 414:303-12. [PMID: 22019473 DOI: 10.1016/j.jmb.2011.10.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Revised: 10/06/2011] [Accepted: 10/09/2011] [Indexed: 10/16/2022]
Abstract
There is strong experimental evidence of the influence of surfactants (e.g., fatty acids) on the kinetics of amyloid fibril formation. However, the structures of mixed assemblies and interactions between surfactants and fibril-forming peptides are still not clear. Here, coarse-grained simulations are employed to study the aggregation kinetics of amyloidogenic peptides in the presence of amphiphilic lipids. The simulations show that the lower the fibril formation propensity of the peptides, the higher the influence of the surfactants on the peptide self-assembly kinetics. In particular, the lag phase of weakly aggregating peptides increases because of the formation of mixed oligomers, which are promoted by hydrophobic interactions and favorable entropy of mixing. A transient peak in the number of surfactants attached to the growing fibril is observed before reaching the mature fibril in some of the simulations. This peak originates from transient fibrillar defects consisting of exposed hydrophobic patches on the fibril surface, which provide a possible explanation for the temporary maximum of fluorescence observed sometimes in kinetic traces of the binding of small-molecule dyes to amyloid fibrils.
Collapse
Affiliation(s)
- Ran Friedman
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
| | | |
Collapse
|
22
|
Eichner T, Radford SE. Understanding the complex mechanisms of β2-microglobulin amyloid assembly. FEBS J 2011; 278:3868-83. [PMID: 21595827 PMCID: PMC3229708 DOI: 10.1111/j.1742-4658.2011.08186.x] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Revised: 05/11/2011] [Accepted: 05/13/2011] [Indexed: 11/30/2022]
Abstract
Several protein misfolding diseases are associated with the conversion of native proteins into ordered protein aggregates known as amyloid. Studies of amyloid assemblies have indicated that non-native proteins are responsible for initiating aggregation in vitro and in vivo. Despite the importance of these species for understanding amyloid disease, the structural and dynamic features of amyloidogenic intermediates and the molecular details of how they aggregate remain elusive. This review focuses on recent advances in developing a molecular description of the folding and aggregation mechanisms of the human amyloidogenic protein β(2)-microglobulin under physiologically relevant conditions. In particular, the structural and dynamic properties of the non-native folding intermediate I(T) and its role in the initiation of fibrillation and the development of dialysis-related amyloidosis are discussed.
Collapse
Affiliation(s)
- Timo Eichner
- Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA.
| | | |
Collapse
|
23
|
Non-esterified fatty acids generate distinct low-molecular weight amyloid-β (Aβ42) oligomers along pathway different from fibril formation. PLoS One 2011; 6:e18759. [PMID: 21526230 PMCID: PMC3079704 DOI: 10.1371/journal.pone.0018759] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2011] [Accepted: 03/09/2011] [Indexed: 12/13/2022] Open
Abstract
Amyloid-β (Aβ) peptide aggregation is known to play a central role in the etiology of Alzheimer’s disease (AD). Among various aggregates, low-molecular weight soluble oligomers of Aβ are increasingly believed to be the primary neurotoxic agents responsible for memory impairment. Anionic interfaces are known to influence the Aβ aggregation process significantly. Here, we report the effects of interfaces formed by medium-chain (C9–C12), saturated non-esterified fatty acids (NEFAs) on Aβ42 aggregation. NEFAs uniquely affected Aβ42 aggregation rates that depended on both the ratio of Aβ:NEFA as well the critical micelle concentration (CMC) of the NEFAs. More importantly, irrespective of the kind of NEFA used, we observed that two distinct oligomers, 12–18 mers and 4–5 mers were formed via different pathway of aggregation under specific experimental conditions: (i) 12–18 mers were generated near the CMC in which NEFAs augment the rate of Aβ42 aggregation towards fibril formation, and, (ii) 4–5 mers were formed above the CMC, where NEFAs inhibit fibril formation. The data indicated that both 12–18 mers and 4–5 mers are formed along an alternate pathway called ‘off-pathway’ that did not result in fibril formation and yet have subtle structural and morphological differences that distinguish their bulk molecular behavior. These observations, (i) reflect the possible mechanism of Aβ aggregation in physiological lipid-rich environments, and (ii) reiterate the fact that all oligomeric forms of Aβ need not be obligatory intermediates of the fibril formation pathway.
Collapse
|
24
|
Ozawa D, Hasegawa K, Lee YH, Sakurai K, Yanagi K, Ookoshi T, Goto Y, Naiki H. Inhibition of beta2-microglobulin amyloid fibril formation by alpha2-macroglobulin. J Biol Chem 2011; 286:9668-76. [PMID: 21216953 DOI: 10.1074/jbc.m110.167965] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The relationship between various amyloidoses and chaperones is gathering attention. In patients with dialysis-related amyloidosis, α(2)-macroglobulin (α2M), an extracellular chaperone, forms a complex with β(2)-microglobulin (β2-m), a major component of amyloid fibrils, but the molecular mechanisms and biological implications of the complex formation remain unclear. Here, we found that α2M substoichiometrically inhibited the β2-m fibril formation at a neutral pH in the presence of SDS, a model for anionic lipids. Binding analysis showed that the binding affinity between α2M and β2-m in the presence of SDS was higher than that in the absence of SDS. Importantly, SDS dissociated tetrameric α2M into dimers with increased surface hydrophobicity. Western blot analysis revealed that both tetrameric and dimeric α2M interacted with SDS-denatured β2-m. At a physiologically relevant acidic pH and in the presence of heparin, α2M was also dissociated into dimers, and both tetrameric and dimeric α2M interacted with β2-m, resulting in the inhibition of fibril growth reaction. These results suggest that under conditions where native β2-m is denatured, tetrameric α2M is also converted to dimeric form with exposed hydrophobic surfaces to favor the hydrophobic interaction with denatured β2-m, thus dimeric α2M as well as tetrameric α2M may play an important role in controlling β2-m amyloid fibril formation.
Collapse
Affiliation(s)
- Daisaku Ozawa
- Department of Pathological Sciences, Faculty of Medical Sciences, University of Fukui, Fukui 910-1193, Japan
| | | | | | | | | | | | | | | |
Collapse
|
25
|
Rennella E, Corazza A, Giorgetti S, Fogolari F, Viglino P, Porcari R, Verga L, Stoppini M, Bellotti V, Esposito G. Folding and fibrillogenesis: clues from beta2-microglobulin. J Mol Biol 2010; 401:286-97. [PMID: 20558175 DOI: 10.1016/j.jmb.2010.06.016] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2010] [Revised: 06/07/2010] [Accepted: 06/08/2010] [Indexed: 11/18/2022]
Abstract
Renal failure impairs the clearance of beta(2)-microglobulin from the serum, with the result that this protein accumulates in joints under the form of amyloid fibrils. While the molecular mechanism leading to deposition of amyloid in vivo is not totally understood, some organic compounds, such as trifluoroethanol (TFE), are commonly used to promote the elongation of amyloid fibrils in vitro. This article gives some insights into the structural properties and the conformational states of beta(2)-microglobulin in the presence of TFE, using both the wild-type protein and the mutant Trp60Gly. The structure of the native state of the protein is rather insensitive to the presence of the alcohol, but the stability of this state is lowered in comparison to some other conformational states. In particular, a native-like folding intermediate is observed in the presence of moderate concentrations of TFE. Instead, at higher concentrations of the alcohol, the population of a disordered native-unlike state is dominant and correlates with the ability to elongate fibrils.
Collapse
Affiliation(s)
- Enrico Rennella
- Dipartimento di Scienze e Tecnologie Biomediche, Università di Udine, I-33100 Udine, Italy
| | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Hiramatsu H, Lu M, Goto Y, Kitagawa T. The β-Sheet Structure pH Dependence of the Core Fragments of β2-Microglobulin Amyloid Fibrils. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2010. [DOI: 10.1246/bcsj.20090317] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
27
|
Hiramatsu H, Lu M, Matsuo K, Gekko K, Goto Y, Kitagawa T. Differences in the molecular structure of beta(2)-microglobulin between two morphologically different amyloid fibrils. Biochemistry 2010; 49:742-51. [PMID: 20028123 DOI: 10.1021/bi901536j] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Differences in the molecular structures of beta(2)-microglobulin between the two morphologically different amyloid fibrils having a needlelike [long-straight (LS)] and flexible [wormlike (WL)] character were investigated by infrared, Raman, and vacuum-ultraviolet circular dichroism spectroscopy. It turned out that although the beta-sheet content was comparable between the two kinds of fibrils (53 +/- 6% for the LS fibril and 47 +/- 6% for the WL fibril), the protonation states of the carboxyl side chains were distinctly different; the deprotonated (COO(-)) and protonated (COOH) forms were dominant in the LS and WL fibrils at pH 2.5, respectively, meaning that the pK(a) is specifically lowered in the LS fibril. Such a difference was not observed for the fibrils of the core fragments. Since site-specific interactions generally cause variation in the pK(a) of carboxyl side chains in proteins, these results suggest that "hook"-like interactions generated by hydrogen bonding and the formation of a salt bridge are present in the LS fibril, providing enthalpic stabilization. Presumably, the carboxyl groups fix the spatial arrangement of beta-strands and beta-sheets, bringing about the needlelike morphology. The absence of this regulation would result in the flexible morphology of the WL fibril, providing entropic stabilization.
Collapse
Affiliation(s)
- Hirotsugu Hiramatsu
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, Okazaki 444-8787, Japan
| | | | | | | | | | | |
Collapse
|
28
|
Amyloid fibrils formed by selective N-, C-terminal sequences of mouse apolipoprotein A-II. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:1517-29. [DOI: 10.1016/j.bbapap.2009.06.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2009] [Revised: 06/02/2009] [Accepted: 06/26/2009] [Indexed: 11/19/2022]
|
29
|
Naiki H, Nagai Y. Molecular pathogenesis of protein misfolding diseases: pathological molecular environments versus quality control systems against misfolded proteins. J Biochem 2009; 146:751-6. [PMID: 19643812 DOI: 10.1093/jb/mvp119] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Diverse human diseases, including various neurodegenerative disorders and amyloidoses, are thought to result from the misfolding and aggregation of disease-causative proteins, and thus are collectively called protein misfolding diseases. Natively folded disease-causative proteins generally undergo a beta-sheet conformational transition through an energetically unfavourable process, and further polymerize into amyloid fibrils. In the case of beta(2)-microglobulin-related amyloidosis, an extracellular protein misfolding disease, many kinds of biological molecules including glycosaminoglycans, proteoglycans and lipids partially unfold beta(2)-microglobulin and catalyse its subsequent nucleus formation. After amyloid fibrils are formed, these biological molecules stabilize the beta(2)-microglobulin fibrils. In the polyglutamine neurodegenerative diseases, an intracellular protein misfolding disease, molecular chaperones as well as the ubiquitin-proteasome and autophagy-lysosome protein degradation systems, which are called the protein quality control systems, strictly regulate protein misfolding, aggregation and disease progression. A family of extracellular chaperones also binds to misfolded proteins and inhibit amyloid fibril formation in the extracellular space. Protein misfolding and aggregation may be an ideal therapeutic target for protein misfolding diseases in general.
Collapse
Affiliation(s)
- Hironobu Naiki
- Division of Molecular Pathology, Department of Pathological Sciences, Faculty of Medical Sciences, University of Fukui, Fukui 910-1193, Japan.
| | | |
Collapse
|
30
|
Abstract
beta(2)-microglobulin (beta(2)m) is capable of forming amyloid in osteoarticular structures in kidney failure patients that undergo chronic hemodialysis treatment. Although sophisticated analytical methods have yielded comprehensive data about the conformation of the native protein both as a monomer and as the light chain of the type I major histocompatibility complex, the cause and mechanisms leading to the transformation of beta(2)m into amyloid deposits in patients with dialysis-related amyloidosis are unsettled. The impact on conformational stability of various truncations, cleavages, amino acid substitutions, and divalent cations, especially Cu(2+), however, are highly relevant for understanding beta(2)m unfolding pathways leading to amyloid formation. This review describes the current knowledge about such conformationally destabilizing and amyloidogenic factors and links these to the structure and function of beta(2)m in normal physiology and pathology. Tables listing modifications of beta(2)m found in amyloid from patients and a systematic overview of laboratory conditions conducive to beta(2)m-fibrillogenesis are also included.
Collapse
|