1
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Behera DP, Subadini S, Freudenberg U, Sahoo H. Sulfation of hyaluronic acid reconfigures the mechanistic pathway of bone morphogenetic protein-2 aggregation. Int J Biol Macromol 2024; 263:130128. [PMID: 38350587 DOI: 10.1016/j.ijbiomac.2024.130128] [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: 11/22/2023] [Revised: 02/03/2024] [Accepted: 02/09/2024] [Indexed: 02/15/2024]
Abstract
Bone morphogenetic protein-2 (BMP-2) is a critical growth factor of bone extracellular matrix (ECM), pivotal for osteogenesis. Glycosaminoglycans (GAGs), another vital ECM biomolecules, interact with growth factors, affecting signal transduction. Our study primarily focused on hyaluronic acid (HA), a prevalent GAG, and its sulfated derivative (SHA). We explored their impact on BMP-2's conformation, aggregation, and mechanistic pathways of aggregation using diverse optical and rheological methods. In the presence of HA and SHA, the secondary structure of BMP-2 underwent a structured transformation, characterized by a substantial increase in beta sheet content, and a detrimental alteration, manifesting as a shift towards unstructured content, respectively. Although both HA and SHA induced BMP-2 aggregation, their mechanisms differed. SHA led to rapid amorphous aggregates, while HA promoted amyloid fibrils with a lag phase and sigmoidal kinetics. Aggregate size and shape varied; HA produced larger structures, SHA smaller. Each aggregation type followed distinct pathways influenced by viscosity and excluded volume. Higher viscosity, low diffusivity of protein and higher excluded volume In the presence of HA promotes fibrillation having size in micrometer range. Low viscosity, high diffusivity of protein and lesser excluded volume leads to amorphous aggregate of size in nanometer range.
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Affiliation(s)
- Devi Prasanna Behera
- Biophysical and Protein Chemistry Lab, Department of Chemistry, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Suchismita Subadini
- Biophysical and Protein Chemistry Lab, Department of Chemistry, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Uwe Freudenberg
- Institute of Polymer Research, Technical University Dresden, 01307 Dresden, Germany
| | - Harekrushna Sahoo
- Biophysical and Protein Chemistry Lab, Department of Chemistry, National Institute of Technology, Rourkela 769008, Odisha, India; Center for Nanomaterials, National Institute of Technology, Rourkela 769008, Odisha, India.
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2
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Dušeková E, Berta M, Sedláková D, Řeha D, Dzurillová V, Shaposhnikova A, Fadaei F, Tomková M, Minofar B, Sedlák E. Specific anion effect on properties of HRV 3C protease. Biophys Chem 2022; 287:106825. [PMID: 35597150 DOI: 10.1016/j.bpc.2022.106825] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/19/2022] [Accepted: 05/07/2022] [Indexed: 12/12/2022]
Abstract
Specific salts effect is intensively studied from the prospective of modification of different physico-chemical properties of biomacromolecules. Limited knowledge of the specific salts effect on enzymes led us to address the influence of five sodium anions: sulfate, phosphate, chloride, bromide, and perchlorate, on catalytic and conformational properties of human rhinovirus-14 (HRV) 3C protease. The enzyme conformation was monitored by circular dichroism spectrum (CD) and by tyrosines fluorescence. Stability and flexibility of the enzyme have been analyzed by CD in the far-UV region, differential scanning calorimetry and molecular dynamics simulations, respectively. We showed significant influence of the anions on the enzyme properties in accordance with the Hofmeister effect. The HRV 3C protease in the presence of kosmotropic anions, in contrast with chaotropic anions, exhibits increased stability, rigidity. Correlations of stabilization effect of anions on the enzyme with their charge density and the rate constant of the enzyme with the viscosity B-coefficients of anions suggest direct interaction of the anions with HRV 3C protease. The role of stabilization and decreased fluctuation of the polypeptide chain of HRV 3C protease on its activation in the presence of kosmotropic anions is discussed within the frame of the macromolecular rate theory.
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Affiliation(s)
- Eva Dušeková
- Department of Biophysics, Faculty of Science, P. J. Šafárik University in Košice, Jesenná 5, 04154 Košice, Slovakia
| | - Martin Berta
- Department of Biophysics, Faculty of Science, P. J. Šafárik University in Košice, Jesenná 5, 04154 Košice, Slovakia
| | - Dagmar Sedláková
- Department of Biophysics, Faculty of Science, P. J. Šafárik University in Košice, Jesenná 5, 04154 Košice, Slovakia; Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 040 01 Košice, Slovakia
| | - David Řeha
- Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 1645/31A, 37005 České Budějovice, Czech Republic
| | - Veronika Dzurillová
- Department of Biophysics, Faculty of Science, P. J. Šafárik University in Košice, Jesenná 5, 04154 Košice, Slovakia
| | - Anastasiia Shaposhnikova
- Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 1645/31A, 37005 České Budějovice, Czech Republic; Laboratory of Structural Biology and Bioinformatics, Institute of Microbiology of the Czech Academy of Sciences, Zámek 136, 37333 Nové Hrady, Czech Republic
| | - Fatemeh Fadaei
- Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 1645/31A, 37005 České Budějovice, Czech Republic; Laboratory of Structural Biology and Bioinformatics, Institute of Microbiology of the Czech Academy of Sciences, Zámek 136, 37333 Nové Hrady, Czech Republic
| | - Mária Tomková
- Centre for Interdisciplinary Biosciences, P. J. Šafárik University in Košice, Jesenná 5, 04154 Košice, Slovakia
| | - Babak Minofar
- Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 1645/31A, 37005 České Budějovice, Czech Republic.
| | - Erik Sedlák
- Centre for Interdisciplinary Biosciences, P. J. Šafárik University in Košice, Jesenná 5, 04154 Košice, Slovakia.
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3
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Dušeková E, Garajová K, Yavaşer R, Tomková M, Sedláková D, Dzurillová V, Kulik N, Fadaei F, Shaposhnikova A, Minofar B, Sedlák E. Modulation of global stability, ligand binding and catalytic properties of trypsin by anions. Biophys Chem 2022; 288:106856. [PMID: 35872468 DOI: 10.1016/j.bpc.2022.106856] [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: 05/08/2022] [Revised: 07/02/2022] [Accepted: 07/13/2022] [Indexed: 12/01/2022]
Abstract
Specific salts effect is well-known on stability and solubility of proteins, however, relatively limited knowledge is known regarding the effect on catalytic properties of enzymes. Here, we examined the effect of four sodium anions on thermal stability and catalytic properties of trypsin and binding of the fluorescent probe, p-aminobenzamidine (PAB), to the enzyme. We show that the specific anions effect on trypsin properties agrees with the localization of the anions in the Hofmeister series. Thermal stability of trypsin, Tm, the affinity of the fluorescent probe to the binding site, Kd, and the rate constant, kcat, of trypsin-catalyzed hydrolysis of the substrate N-benzoyl-L-arginine ethyl ester (BAEE) increase with increasing kosmotropic character of anions in the order: perchlorate<bromide<chloride<sulfate, while the value of Michaelis constant, KM, decreases. Correlations between the values of Tm, Kd for PAB, kcat, and KM for BAEE in the presence of 1 M studied salts suggest interrelation among these parameters of the enzyme. Global stabilization as well as increased rigidity of trypsin is accompanied by strengthening of interaction with fluorescent probe PAB and in accordance with decreasing values of KM for the substrate BAEE. Strong correlations between parameters characterizing the trypsin properties with the charge densities of anions clearly indicate direct electrostatic interaction as a basis of the specific anion effect on the conformational and functional properties of the enzyme.
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Affiliation(s)
- Eva Dušeková
- Department of Biophysics, Faculty of Science, P. J. Šafárik University in Košice, Jesenná 5, 04154 Košice, Slovakia
| | - Katarína Garajová
- Department of Biochemistry, Faculty of Science, P. J. Šafárik University in Košice, Moyzesova 11, 04154 Košice, Slovakia
| | - Rukiye Yavaşer
- Department of Biochemistry, Faculty of Science, P. J. Šafárik University in Košice, Moyzesova 11, 04154 Košice, Slovakia; Chemistry Department, Faculty of Arts and Science, Aydın Adnan Menderes University, 09010 Aydın, Turkey
| | - Mária Tomková
- Center for Interdisciplinary Biosciences, P. J. Šafárik University in Košice, Jesenná 5, 04154 Košice, Slovakia
| | - Dagmar Sedláková
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 040 01 Košice, Slovakia
| | - Veronika Dzurillová
- Department of Biophysics, Faculty of Science, P. J. Šafárik University in Košice, Jesenná 5, 04154 Košice, Slovakia
| | - Natalia Kulik
- Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 1645/31A, 37005 České Budějovice, Czech Republic
| | - Fatemeh Fadaei
- Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 1645/31A, 37005 České Budějovice, Czech Republic; Laboratory of Structural Biology and Bioinformatics, Institute of Microbiology of the Czech Academy of Sciences, Zámek 136, 37333 Nové Hrady, Czech Republic
| | - Anastasiia Shaposhnikova
- Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 1645/31A, 37005 České Budějovice, Czech Republic; Laboratory of Structural Biology and Bioinformatics, Institute of Microbiology of the Czech Academy of Sciences, Zámek 136, 37333 Nové Hrady, Czech Republic
| | - Babak Minofar
- Laboratory of Structural Biology and Bioinformatics, Institute of Microbiology of the Czech Academy of Sciences, Zámek 136, 37333 Nové Hrady, Czech Republic.
| | - Erik Sedlák
- Center for Interdisciplinary Biosciences, P. J. Šafárik University in Košice, Jesenná 5, 04154 Košice, Slovakia.
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4
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Yao W, Wang K, Wu A, Reed WF, Gibb BC. Anion binding to ubiquitin and its relevance to the Hofmeister effects. Chem Sci 2020; 12:320-330. [PMID: 34163600 PMCID: PMC8178748 DOI: 10.1039/d0sc04245e] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/29/2020] [Indexed: 02/01/2023] Open
Abstract
Although the non-covalent interactions between proteins and salts contributing to the Hofmeister effects have been generally mapped, there are many questions regarding the specifics of these interactions. We report here studies involving the small protein ubiquitin and salts of polarizable anions. These studies reveal a complex interplay between the reverse Hofmeister effect at low pH, the salting-in Hofmeister effect at higher pH, and six anion binding sites in ubiquitin at the root of these phenomena. These sites are all located at protuberances of preorganized secondary structure, and although stronger at low pH, are still apparent when ubiquitin possesses no net charge. These results demonstrate the traceability of these Hofmeister phenomena and suggest new strategies for understanding the supramolecular properties of proteins.
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Affiliation(s)
- Wei Yao
- Department of Chemistry, Tulane University New Orleans LA 70118 USA
| | - Kaiyu Wang
- Department of Chemistry, Tulane University New Orleans LA 70118 USA
| | - Aide Wu
- Department of Physics and Engineering Physics, Tulane University New Orleans LA 70118 USA
| | - Wayne F Reed
- Department of Physics and Engineering Physics, Tulane University New Orleans LA 70118 USA
| | - Bruce C Gibb
- Department of Chemistry, Tulane University New Orleans LA 70118 USA
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5
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Donnarumma F, Leone S, Delfi M, Emendato A, Ami D, Laurents DV, Natalello A, Spadaccini R, Picone D. Probing structural changes during amyloid aggregation of the sweet protein MNEI. FEBS J 2019; 287:2808-2822. [DOI: 10.1111/febs.15168] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/20/2019] [Accepted: 12/05/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Federica Donnarumma
- Department of Chemical Sciences University of Naples ‘Federico II’ Napoli Italy
| | - Serena Leone
- Department of Chemical Sciences University of Naples ‘Federico II’ Napoli Italy
| | - Masoud Delfi
- Department of Chemical Sciences University of Naples ‘Federico II’ Napoli Italy
| | - Alessandro Emendato
- Department of Chemical Sciences University of Naples ‘Federico II’ Napoli Italy
| | - Diletta Ami
- Department of Biotechnology and Biosciences University of Milano‐Bicocca Italy
| | - Douglas V. Laurents
- Institute of Physical Chemistry ‘Rocasolano’ Consejo Superior de Investigaciones Científicas Madrid Spain
| | - Antonino Natalello
- Department of Biotechnology and Biosciences University of Milano‐Bicocca Italy
| | - Roberta Spadaccini
- Department of Science and Technology Università degli Studi del Sannio Benevento Italy
| | - Delia Picone
- Department of Chemical Sciences University of Naples ‘Federico II’ Napoli Italy
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6
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Sedlák E, Sedláková D, Marek J, Hančár J, Garajová K, Žoldák G. Ion-Specific Protein/Water Interface Determines the Hofmeister Effect on the Kinetic Stability of Glucose Oxidase. J Phys Chem B 2019; 123:7965-7973. [DOI: 10.1021/acs.jpcb.9b05195] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Erik Sedlák
- Center for Interdisciplinary Biosciences, Technology and Innovation Park P.J. Šafárik University, Jesenna 5, 041 54 Košice, Slovakia
- Department of Biochemistry, Faculty of Science, P. J. Šafárik University in Košice, Moyzesova 11, 04001 Košice, Slovakia
| | - Dagmar Sedláková
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 04001 Košice, Slovakia
| | - Jozef Marek
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 04001 Košice, Slovakia
| | - Jozef Hančár
- Department of Biochemistry, Faculty of Science, P. J. Šafárik University in Košice, Moyzesova 11, 04001 Košice, Slovakia
| | - Katarína Garajová
- Department of Biochemistry, Faculty of Science, P. J. Šafárik University in Košice, Moyzesova 11, 04001 Košice, Slovakia
| | - Gabriel Žoldák
- Center for Interdisciplinary Biosciences, Technology and Innovation Park P.J. Šafárik University, Jesenna 5, 041 54 Košice, Slovakia
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7
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Lin Y, Sahoo BR, Ozawa D, Kinoshita M, Kang J, Lim MH, Okumura M, Huh YH, Moon E, Jang JH, Lee HJ, Ryu KY, Ham S, Won HS, Ryu KS, Sugiki T, Bang JK, Hoe HS, Fujiwara T, Ramamoorthy A, Lee YH. Diverse Structural Conversion and Aggregation Pathways of Alzheimer's Amyloid-β (1-40). ACS NANO 2019; 13:8766-8783. [PMID: 31310506 DOI: 10.1021/acsnano.9b01578] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Complex amyloid aggregation of amyloid-β (1-40) (Aβ1-40) in terms of monomer structures has not been fully understood. Herein, we report the microscopic mechanism and pathways of Aβ1-40 aggregation with macroscopic viewpoints through tuning its initial structure and solubility. Partial helical structures of Aβ1-40 induced by low solvent polarity accelerated cytotoxic Aβ1-40 amyloid fibrillation, while predominantly helical folds did not aggregate. Changes in the solvent polarity caused a rapid formation of β-structure-rich protofibrils or oligomers via aggregation-prone helical structures. Modulation of the pH and salt concentration transformed oligomers to protofibrils, which proceeded to amyloid formation. We reveal diverse molecular mechanisms underlying Aβ1-40 aggregation with conceptual energy diagrams and propose that aggregation-prone partial helical structures are key to inducing amyloidogenesis. We demonstrate that context-dependent protein aggregation is comprehensively understood using the macroscopic phase diagram, which provides general insights into differentiation of amyloid formation and phase separation from unfolded and folded structures.
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Affiliation(s)
- Yuxi Lin
- Department of Chemistry , Sookmyung Women's University , Cheongpa-ro 47-gil 100 , Yongsan-gu, Seoul 04310 , South Korea
| | - Bikash R Sahoo
- Biophysics Program and Department of Chemistry, Biomedical Engineering, and Macromolecular Science and Engineering , University of Michigan , Ann Arbor , Michigan 48109-1055 , United States
| | - Daisaku Ozawa
- Department of Neurotherapeutics , Osaka University Graduate School of Medicine , 2-2 Yamadaoka , Suita , Osaka 565-0871 , Japan
| | - Misaki Kinoshita
- Frontier Research Institute for Interdisciplinary Sciences , Tohoku University , 6-3 Aramaki-Aza-Aoba , Aoba-ku, Sendai 980-8578 , Japan
| | - Juhye Kang
- Department of Chemistry , Korea Advanced Institute of Science and Technology , Daejeon 34141 , South Korea
- Department of Chemistry , Ulsan National Institute of Science and Technology , Ulsan 44919 , South Korea
| | - Mi Hee Lim
- Department of Chemistry , Korea Advanced Institute of Science and Technology , Daejeon 34141 , South Korea
| | - Masaki Okumura
- Frontier Research Institute for Interdisciplinary Sciences , Tohoku University , 6-3 Aramaki-Aza-Aoba , Aoba-ku, Sendai 980-8578 , Japan
| | | | | | | | - Hyun-Ju Lee
- Department of Neural Development and Disease , Korea Brain Research Institute , 61 Cheomdan-ro , Dong-gu, Daegu 41068 , South Korea
| | - Ka-Young Ryu
- Department of Neural Development and Disease , Korea Brain Research Institute , 61 Cheomdan-ro , Dong-gu, Daegu 41068 , South Korea
| | - Sihyun Ham
- Department of Chemistry , Sookmyung Women's University , Cheongpa-ro 47-gil 100 , Yongsan-gu, Seoul 04310 , South Korea
| | - Hyung-Sik Won
- Department of Biotechnology, Research Institute and College of Biomedical and Health Science , Konkuk University , Chungju , Chungbuk 27478 , South Korea
| | | | - Toshihiko Sugiki
- Institute for Protein Research , Osaka University , Yamadaoka 3-2 , Suita , Osaka 565-0871 , Japan
| | | | - Hyang-Sook Hoe
- Department of Neural Development and Disease , Korea Brain Research Institute , 61 Cheomdan-ro , Dong-gu, Daegu 41068 , South Korea
| | - Toshimichi Fujiwara
- Institute for Protein Research , Osaka University , Yamadaoka 3-2 , Suita , Osaka 565-0871 , Japan
| | - Ayyalusamy Ramamoorthy
- Biophysics Program and Department of Chemistry, Biomedical Engineering, and Macromolecular Science and Engineering , University of Michigan , Ann Arbor , Michigan 48109-1055 , United States
| | - Young-Ho Lee
- Institute for Protein Research , Osaka University , Yamadaoka 3-2 , Suita , Osaka 565-0871 , Japan
- Bio-Analytical Science , University of Science and Technology , Daejeon 34113 , South Korea
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8
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Wang W, Ohtake S. Science and art of protein formulation development. Int J Pharm 2019; 568:118505. [PMID: 31306712 DOI: 10.1016/j.ijpharm.2019.118505] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 07/08/2019] [Accepted: 07/08/2019] [Indexed: 02/07/2023]
Abstract
Protein pharmaceuticals have become a significant class of marketed drug products and are expected to grow steadily over the next decade. Development of a commercial protein product is, however, a rather complex process. A critical step in this process is formulation development, enabling the final product configuration. A number of challenges still exist in the formulation development process. This review is intended to discuss these challenges, to illustrate the basic formulation development processes, and to compare the options and strategies in practical formulation development.
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Affiliation(s)
- Wei Wang
- Biological Development, Bayer USA, LLC, 800 Dwight Way, Berkeley, CA 94710, United States.
| | - Satoshi Ohtake
- Pharmaceutical Research and Development, Pfizer Biotherapeutics Pharmaceutical Sciences, Chesterfield, MO 63017, United States
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9
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Dušeková E, Garajová K, Yavaşer R, Varhač R, Sedlák E. Hofmeister effect on catalytic properties of chymotrypsin is substrate-dependent. Biophys Chem 2018; 243:8-16. [DOI: 10.1016/j.bpc.2018.10.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 09/30/2018] [Accepted: 10/09/2018] [Indexed: 12/26/2022]
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10
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Wang W, Roberts CJ. Protein aggregation – Mechanisms, detection, and control. Int J Pharm 2018; 550:251-268. [DOI: 10.1016/j.ijpharm.2018.08.043] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 08/18/2018] [Accepted: 08/20/2018] [Indexed: 12/19/2022]
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11
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Garajová K, Balogová A, Dušeková E, Sedláková D, Sedlák E, Varhač R. Correlation of lysozyme activity and stability in the presence of Hofmeister series anions. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:281-288. [DOI: 10.1016/j.bbapap.2016.11.016] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 11/01/2016] [Accepted: 11/28/2016] [Indexed: 01/01/2023]
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12
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Giraldo R, Fernández C, Moreno-del Álamo M, Molina-García L, Revilla-García A, Sánchez-Martínez MC, Giménez-Abián JF, Moreno-Díaz de la Espina S. RepA-WH1 prionoid: Clues from bacteria on factors governing phase transitions in amyloidogenesis. Prion 2017; 10:41-9. [PMID: 27040981 PMCID: PMC4981189 DOI: 10.1080/19336896.2015.1129479] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
In bacterial plasmids, Rep proteins initiate DNA replication by undergoing a structural transformation coupled to dimer dissociation. Amyloidogenesis of the ‘winged-helix’ N-terminal domain of RepA (WH1) is triggered in vitro upon binding to plasmid-specific DNA sequences, and occurs at the bacterial nucleoid in vivo. Amyloid fibers are made of distorted RepA-WH1 monomers that assemble as single or double intertwined tubular protofilaments. RepA-WH1 causes in E. coli an amyloid proteinopathy, which is transmissible from mother to daughter cells, but not infectious, and enables conformational imprinting in vitro and in vivo; i.e. RepA-WH1 is a ‘prionoid’. Microfluidics allow the assessment of the intracellular dynamics of RepA-WH1: bacterial lineages maintain two types (strains-like) of RepA-WH1 amyloids, either multiple compact cytotoxic particles or a single aggregate with the appearance of a fluidized hydrogel that it is mildly detrimental to growth. The Hsp70 chaperone DnaK governs the phase transition between both types of RepA-WH1 aggregates in vivo, thus modulating the vertical propagation of the prionoid. Engineering chimeras between the Sup35p/[PSI+] prion and RepA-WH1 generates [REP-PSI+], a synthetic prion exhibiting strong and weak phenotypic variants in yeast. These recent findings on a synthetic, self-contained bacterial prionoid illuminate central issues of protein amyloidogenesis.
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Affiliation(s)
- Rafael Giraldo
- a Department of Cellular & Molecular Biology , Centro de Investigaciones Biológicas - CSIC , Madrid , Spain
| | - Cristina Fernández
- a Department of Cellular & Molecular Biology , Centro de Investigaciones Biológicas - CSIC , Madrid , Spain
| | - María Moreno-del Álamo
- a Department of Cellular & Molecular Biology , Centro de Investigaciones Biológicas - CSIC , Madrid , Spain
| | - Laura Molina-García
- a Department of Cellular & Molecular Biology , Centro de Investigaciones Biológicas - CSIC , Madrid , Spain
| | - Aída Revilla-García
- a Department of Cellular & Molecular Biology , Centro de Investigaciones Biológicas - CSIC , Madrid , Spain
| | | | - Juan F Giménez-Abián
- a Department of Cellular & Molecular Biology , Centro de Investigaciones Biológicas - CSIC , Madrid , Spain
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13
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Nespovitaya N, Gath J, Barylyuk K, Seuring C, Meier BH, Riek R. Dynamic Assembly and Disassembly of Functional β-Endorphin Amyloid Fibrils. J Am Chem Soc 2016; 138:846-56. [DOI: 10.1021/jacs.5b08694] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nadezhda Nespovitaya
- Laboratory
of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Julia Gath
- Laboratory
of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Konstantin Barylyuk
- Laboratory
of Organic Chemistry, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Carolin Seuring
- Laboratory
of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Beat H. Meier
- Laboratory
of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Roland Riek
- Laboratory
of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
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14
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De Leon Rodriguez LM, Hemar Y, Cornish J, Brimble MA. Structure–mechanical property correlations of hydrogel forming β-sheet peptides. Chem Soc Rev 2016; 45:4797-824. [DOI: 10.1039/c5cs00941c] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
This review discusses about β-sheet peptide structure at the molecular level and the bulk mechanical properties of the corresponding hydrogels.
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Affiliation(s)
| | - Yacine Hemar
- School of Chemical Sciences
- The University of Auckland
- Auckland
- New Zealand
- The Riddet Institute
| | - Jillian Cornish
- Department of Medicine
- The University of Auckland
- Auckland
- New Zealand
| | - Margaret A. Brimble
- School of Chemical Sciences
- The University of Auckland
- Auckland
- New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery
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15
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Abstract
In Escherichia coli, hydrogen metabolism plays a prominent role in anaerobic physiology. The genome contains the capability to produce and assemble up to four [NiFe]-hydrogenases, each of which are known, or predicted, to contribute to different aspects of cellular metabolism. In recent years, there have been major advances in the understanding of the structure, function, and roles of the E. coli [NiFe]-hydrogenases. The membrane-bound, periplasmically oriented, respiratory Hyd-1 isoenzyme has become one of the most important paradigm systems for understanding an important class of oxygen-tolerant enzymes, as well as providing key information on the mechanism of hydrogen activation per se. The membrane-bound, periplasmically oriented, Hyd-2 isoenzyme has emerged as an unusual, bidirectional redox valve able to link hydrogen oxidation to quinone reduction during anaerobic respiration, or to allow disposal of excess reducing equivalents as hydrogen gas. The membrane-bound, cytoplasmically oriented, Hyd-3 isoenzyme is part of the formate hydrogenlyase complex, which acts to detoxify excess formic acid under anaerobic fermentative conditions and is geared towards hydrogen production under those conditions. Sequence identity between some Hyd-3 subunits and those of the respiratory NADH dehydrogenases has led to hypotheses that the activity of this isoenzyme may be tightly coupled to the formation of transmembrane ion gradients. Finally, the E. coli genome encodes a homologue of Hyd-3, termed Hyd-4, however strong evidence for a physiological role for E. coli Hyd-4 remains elusive. In this review, the versatile hydrogen metabolism of E. coli will be discussed and the roles and potential applications of the spectrum of different types of [NiFe]-hydrogenases available will be explored.
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Owczarz M, Arosio P. Sulfate anion delays the self-assembly of human insulin by modifying the aggregation pathway. Biophys J 2015; 107:197-207. [PMID: 24988354 DOI: 10.1016/j.bpj.2014.05.030] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 04/01/2014] [Accepted: 05/06/2014] [Indexed: 12/18/2022] Open
Abstract
The understanding of the molecular mechanisms underlying protein self-assembly and of their dependence on solvent composition has implications in a large number of biological and biotechnological systems. In this work, we characterize the aggregation process of human insulin at acidic pH in the presence of sulfate ions using a combination of Thioflavin T fluorescence, dynamic light scattering, size exclusion chromatography, Fourier transform infrared spectroscopy, and transmission electron microscopy. It is found that the increase of sulfate concentration inhibits the conversion of insulin molecules into aggregates by modifying the aggregation pathway. At low sulfate concentrations (0-5 mM) insulin forms amyloid fibrils following the nucleated polymerization mechanism commonly observed under acidic conditions in the presence of monovalent anions. When the sulfate concentration is increased above 5 mM, the sulfate anion induces the salting-out of ∼18-20% of insulin molecules into reversible amorphous aggregates, which retain a large content of α-helix structures. During time these aggregates undergo structure rearrangements into β-sheet structures, which are able to recruit monomers and bind to the Thioflavin T dye. The alternative aggregation mechanism observed at large sulfate concentrations is characterized by a larger activation energy and leads to more polymorphic structures with respect to the self-assembly in the presence of chloride ions. The system shown in this work represents a case where amorphous aggregates on pathway to the formation of structures with amyloid features could be detected and analyzed.
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Affiliation(s)
- Marta Owczarz
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland.
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17
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Carballo-Pacheco M, Ismail AE, Strodel B. Oligomer Formation of Toxic and Functional Amyloid Peptides Studied with Atomistic Simulations. J Phys Chem B 2015; 119:9696-705. [PMID: 26130191 DOI: 10.1021/acs.jpcb.5b04822] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Amyloids are associated with diseases, including Alzheimer's, as well as functional roles such as storage of peptide hormones. It is still unclear what differences exist between aberrant and functional amyloids. However, it is known that soluble oligomers formed during amyloid aggregation are more toxic than the final fibrils. Here, we perform molecular dynamics simulations to study the aggregation of the amyloid-β peptide Aβ25-35, associated with Alzheimer's disease, and two functional amyloid-forming tachykinin peptides: kassinin and neuromedin K. Although the three peptides have similar primary sequences, tachykinin peptides, in contrast to Aβ25-35, form nontoxic amyloids. Our simulations reveal that the charge of the C-terminus is essential to controlling the aggregation process. In particular, when the kassinin C-terminus is not amidated, the aggregation kinetics decreases considerably. In addition, we observe that the monomeric peptides in extended conformations aggregate faster than those in collapsed hairpin-like conformations.
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Affiliation(s)
- Martín Carballo-Pacheco
- †AICES Graduate School and Aachener Verfahrenstechnik: Molecular Simulations and Transformations, RWTH Aachen University, Schinkelstraße 2, 52062 Aachen, Germany.,‡Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Ahmed E Ismail
- †AICES Graduate School and Aachener Verfahrenstechnik: Molecular Simulations and Transformations, RWTH Aachen University, Schinkelstraße 2, 52062 Aachen, Germany
| | - Birgit Strodel
- ‡Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.,¶Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Universitätstraße 1, 40225 Düsseldorf, Germany
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18
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Lysozyme stability and amyloid fibrillization dependence on Hofmeister anions in acidic pH. J Biol Inorg Chem 2015; 20:921-33. [DOI: 10.1007/s00775-015-1276-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 05/31/2015] [Indexed: 10/23/2022]
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19
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Arosio P, Knowles TPJ, Linse S. On the lag phase in amyloid fibril formation. Phys Chem Chem Phys 2015; 17:7606-18. [PMID: 25719972 PMCID: PMC4498454 DOI: 10.1039/c4cp05563b] [Citation(s) in RCA: 527] [Impact Index Per Article: 58.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 02/03/2015] [Indexed: 12/11/2022]
Abstract
The formation of nanoscale amyloid fibrils from normally soluble peptides and proteins is a common form of self-assembly phenomenon that has fundamental connections with biological functions and human diseases. The kinetics of this process has been widely studied and exhibits on a macroscopic level three characteristic stages: a lag phase, a growth phase and a final plateau regime. The question of which molecular events take place during each one of these phases has been a central element in the quest for a mechanism of amyloid formation. In this review, we discuss the nature and molecular origin of the lag-phase in amyloid formation by making use of tools and concepts from physical chemistry, in particular from chemical reaction kinetics. We discuss how, in macroscopic samples, it has become apparent that the lag-phase is not a waiting time for nuclei to form. Rather, multiple parallel processes exist and typically millions of primary nuclei form during the lag phase from monomers in solution. Thus, the lag-time represents a time that is required for the nuclei that are formed early on in the reaction to grow and proliferate in order to reach an aggregate concentration that is readily detected in bulk assays. In many cases, this proliferation takes place through secondary nucleation, where fibrils may present a catalytic surface for the formation of new aggregates. Fibrils may also break (fragmentation) and thereby provide new ends for elongation. Thus, at least two - primary nucleation and elongation - and in many systems at least four - primary nucleation, elongation, secondary nucleation and fragmentation - microscopic processes occur during the lag phase. Moreover, these same processes occur during all three phases of the macroscopic aggregation process, albeit at different rates as governed by rate constants and by the concentration of reacting species at each point in time.
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Affiliation(s)
- Paolo Arosio
- Chemistry Department , University of Cambridge , Lensfield road , Cambridge , UK
| | - Tuomas P. J. Knowles
- Chemistry Department , University of Cambridge , Lensfield road , Cambridge , UK
| | - Sara Linse
- Department of Biochemistry and Structural Biology , Chemical Centre , Lund University , P. O. Box 124 , SE221 00 Lund , Sweden .
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20
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Torreira E, Moreno-Del Álamo M, Fuentes-Perez ME, Fernández C, Martín-Benito J, Moreno-Herrero F, Giraldo R, Llorca O. Amyloidogenesis of bacterial prionoid RepA-WH1 recapitulates dimer to monomer transitions of RepA in DNA replication initiation. Structure 2014; 23:183-189. [PMID: 25543255 DOI: 10.1016/j.str.2014.11.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 11/03/2014] [Accepted: 11/06/2014] [Indexed: 01/14/2023]
Abstract
Most available structures of amyloids correspond to peptide fragments that self-assemble in extended cross β sheets. However, structures in which a whole protein domain acts as building block of an amyloid fiber are scarce, in spite of their relevance to understand amyloidogenesis. Here, we use electron microscopy (EM) and atomic force microscopy (AFM) to analyze the structure of amyloid filaments assembled by RepA-WH1, a winged-helix domain from a DNA replication initiator in bacterial plasmids. RepA-WH1 functions as a cytotoxic bacterial prionoid that recapitulates features of mammalian amyloid proteinopathies. RepA are dimers that monomerize at the origin to initiate replication, and we find that RepA-WH1 reproduces this transition to form amyloids. RepA-WH1 assembles double helical filaments by lateral association of a single-stranded precursor built by monomers. Double filaments then associate in mature fibers. The intracellular and cytotoxic RepA-WH1 aggregates might reproduce the hierarchical assembly of human amyloidogenic proteins.
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Affiliation(s)
- Eva Torreira
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - María Moreno-Del Álamo
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Maria Eugenia Fuentes-Perez
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Darwin 3, 28049 Madrid, Spain
| | - Cristina Fernández
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Jaime Martín-Benito
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Darwin 3, 28049 Madrid, Spain
| | - Fernando Moreno-Herrero
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Darwin 3, 28049 Madrid, Spain
| | - Rafael Giraldo
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain.
| | - Oscar Llorca
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain.
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Ruzafa D, Conejero-Lara F, Morel B. Modulation of the stability of amyloidogenic precursors by anion binding strongly influences the rate of amyloid nucleation. Phys Chem Chem Phys 2014; 15:15508-17. [PMID: 23942905 DOI: 10.1039/c3cp52313f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A deep understanding of the physicochemical factors modulating amyloid aggregation of proteins is crucial to develop therapeutic and preventive approaches for amyloid-related diseases. The earliest molecular events of the aggregation cascade represent some of the main targets as indicated by the toxic nature of certain early oligomers. Here, we study how different types of salt ions influence the kinetics of amyloid assembly of the N47A mutant α-spectrin SH3 domain using a battery of techniques. The salts influenced aggregation rates to different extents without altering the overall mechanism and the high apparent order of the experimental kinetics. A quantitative analysis of the initial aggregation rates measured by thioflavine-T fluorescence using a simple nucleation model allowed us to estimate the kinetic and thermodynamic magnitudes of crucial aggregation precursors, as well as to evaluate the impact of each type of ion on the earliest amyloid nucleation stages. Whilst cations did not have any noticeable effect under our experimental conditions, anions stabilized an amyloidogenic intermediate state and also increased the rate of the conformational conversion from dynamic oligomers to amyloid nuclei, resulting in a strong acceleration of the nucleation process. Anions appear to act by preferential binding to the amyloidogenic intermediate state, thus enhancing its population and subsequent oligomerization. Overall, our results contribute to the rationalization of the effect of ions on the amyloid nucleation stage and give insight into the properties of the crucial intermediate precursors of amyloid aggregation.
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Affiliation(s)
- David Ruzafa
- Departamento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain.
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Drazic A, Gebendorfer KM, Mak S, Steiner A, Krause M, Bepperling A, Winter J. Tetramers are the activation-competent species of the HOCl-specific transcription factor HypT. J Biol Chem 2013; 289:977-86. [PMID: 24275662 DOI: 10.1074/jbc.m113.521401] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Hypochlorous acid (HOCl) is an important component of the immune system and is produced by neutrophils to kill invading microorganisms. The transcription factor HypT is specifically activated by HOCl by methionine oxidation and protects Escherichia coli cells from the detrimental effects of HOCl. HypT forms dodecameric ring-like oligomers. Binding of HypT to DNA induces dissociation of the dodecamers into dimers and tetramers, thus forming the DNA-binding species. To dissect HypT dissociation, binding to DNA, and activation, we aimed to dissociate the dodecamers independently of DNA and to analyze HOCl-dependent activation in vitro. We found that HypT dodecamers dissociated into tetramers in the presence of l-arginine and NaCl, which was reversible upon dilution of the additive. Making use of the reversible dissociation, we generated mixed assemblies consisting of wild-type and mutant HypT subunits and determined that mutant subunits with reduced thermal stability were stabilized by wild-type HypT in the mixed assembly. HypT tetramers, as present at high NaCl concentrations, were stabilized against thermal unfolding and aggregation triggered by high HOCl concentrations. Importantly, in vitro activation by HOCl of HypT tetramers was completed within 1 min, whereas activation of dodecamers required 1 h for completion. Furthermore, activation of HypT tetramers required stoichiometric amounts of HOCl instead of an excess of HOCl, as observed for dodecamers. This supports the idea that small HypT oligomers are the activation-competent species, whereas the dodecamers are a storage form. Our study reveals the importance of the dynamic oligomeric state for HypT activation by HOCl.
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Affiliation(s)
- Adrian Drazic
- From the Center for Integrated Protein Science Munich (CiPS), Department Chemie, Technische Universität München, 85747 Garching, Germany
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