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Hribar-Lee B, Lukšič M. Biophysical Principles Emerging from Experiments on Protein-Protein Association and Aggregation. Annu Rev Biophys 2024; 53:1-18. [PMID: 37906740 DOI: 10.1146/annurev-biophys-030722-111729] [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] [Indexed: 11/02/2023]
Abstract
Protein-protein association and aggregation are fundamental processes that play critical roles in various biological phenomena, from cellular signaling to disease progression. Understanding the underlying biophysical principles governing these processes is crucial for elucidating their mechanisms and developing strategies for therapeutic intervention. In this review, we provide an overview of recent experimental studies focused on protein-protein association and aggregation. We explore the key biophysical factors that influence these processes, including protein structure, conformational dynamics, and intermolecular interactions. We discuss the effects of environmental conditions such as temperature, pH and related buffer-specific effects, and ionic strength and related ion-specific effects on protein aggregation. The effects of polymer crowders and sugars are also addressed. We list the techniques used to study aggregation. We analyze emerging trends and challenges in the field, including the development of computational models and the integration of multidisciplinary approaches for a comprehensive understanding of protein-protein association and aggregation.
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Affiliation(s)
- Barbara Hribar-Lee
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia;
| | - Miha Lukšič
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia;
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2
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Mitra A, Naik L, Dhiman R, Sarkar N. Protonation-State Dependent Modulation of Hen Egg-White Lysozyme Fibrillation under the Influence of a Short Synthetic Peptide. J Phys Chem B 2024; 128:5995-6013. [PMID: 38875472 DOI: 10.1021/acs.jpcb.4c01578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2024]
Abstract
Under the influence of various conditions, misfolding of soluble proteins occurs, leading to the formation of toxic insoluble amyloids. The formation and deposition of such amyloids within the body are associated with detrimental biological consequences such as the onset of several amyloid-related diseases. Previously, we established a strategy for the rational design of peptide inhibitors against amyloid formation based on the amyloidogenic-prone region of the protein. In the current study, we have designed and identified an Asp-containing rationally designed hexapeptide (SqP4) as an excellent inhibitor of hen egg-white lysozyme (HEWL) amyloid progression in vitro. First, SqP4 showed strong affinity toward the native monomeric HEWL leading to the stabilization of the native form and restriction in the unfolding process of monomeric HEWL. Second, SqP4 was found to arrest the amyloidogenic misfolded structure of HEWL in a nonfibrillar monomer-like stage. We also observed the differential effect of the protonation state of the charged amino acid (Asp) within the peptide inhibitor on the amyloid formation of HEWL and explored the reason behind the observations. The findings of this study can be implemented in future strategies for the development of potent therapeutics against other amyloid-related diseases.
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Affiliation(s)
- Amit Mitra
- Department of Biotechnology and Medical Engineering, National Institute of Technology Rourkela, Rourkela 769008, Odisha, India
| | - Lincoln Naik
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology Rourkela, Rourkela 769008, Odisha, India
| | - Rohan Dhiman
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology Rourkela, Rourkela 769008, Odisha, India
| | - Nandini Sarkar
- Department of Biotechnology and Medical Engineering, National Institute of Technology Rourkela, Rourkela 769008, Odisha, India
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3
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Li T, Wang D, Zhang X, Chen Z, Wang L. Specific ions effect on aggregation behaviors and structural changes of amyloid fibrils from rice glutelin. Food Chem 2024; 441:138351. [PMID: 38218147 DOI: 10.1016/j.foodchem.2023.138351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/26/2023] [Accepted: 12/31/2023] [Indexed: 01/15/2024]
Abstract
Metal ions have been considered as an important factor on fibrils assembly. Herein, a comprehensive analysis of specific ions effect on fibril formation and structural changes was investigated. The addition of ions (except Zn2+) accelerated the aggregation kinetics of rice glutelin fibrils (RGFs) from 0.93 to 1.28-2.19 h-1. In addition, the fibrillization rate followed the order of NH4+ > Li+ > Na+ > K+ > Cu2+ > Mg2+ > Ca2+ > Zn2+. The highest yield and length of fibrils were observed with Ca2+, probably due to the ionic bridging effect and hydrated capacity of Ca2+. However, Cu2+ reduced the fibrils yield, which was attributable to the fact that Cu2+ disrupted β-sheet structure and inhibited the transition of monomer to fibrils. The polymorphism of fibrils was observed with different salts, and the light metals presented a superior effect on fibrils formation than heavy metals. Overall, this work will provide a further information into how to tune the structure of RGFs using various ions.
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Affiliation(s)
- Ting Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Lihu Road 1800, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Lihu Road 1800, Wuxi 214122, China; Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Lihu Road 1800, Wuxi 214122, China
| | - Dong Wang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Lihu Road 1800, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Lihu Road 1800, Wuxi 214122, China; Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Lihu Road 1800, Wuxi 214122, China
| | - Xinxia Zhang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Lihu Road 1800, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Lihu Road 1800, Wuxi 214122, China; Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Lihu Road 1800, Wuxi 214122, China
| | - Zhengxing Chen
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Lihu Road 1800, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Lihu Road 1800, Wuxi 214122, China; Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Lihu Road 1800, Wuxi 214122, China; State Key Laboratory of Food Science and Resources, Jiangnan University, Lihu Road 1800, Wuxi 214122, China
| | - Li Wang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Lihu Road 1800, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Lihu Road 1800, Wuxi 214122, China; Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Lihu Road 1800, Wuxi 214122, China; State Key Laboratory of Food Science and Resources, Jiangnan University, Lihu Road 1800, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Lihu Road 1800, Wuxi 214122, China.
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Perxés Perich M, Palma-Florez S, Solé C, Goberna-Ferrón S, Samitier J, Gómez-Romero P, Mir M, Lagunas A. Polyoxometalate-Decorated Gold Nanoparticles Inhibit β-Amyloid Aggregation and Cross the Blood-Brain Barrier in a µphysiological Model. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:2697. [PMID: 37836338 PMCID: PMC10574493 DOI: 10.3390/nano13192697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 09/24/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023]
Abstract
Alzheimer's disease is characterized by a combination of several neuropathological hallmarks, such as extracellular aggregates of beta amyloid (Aβ). Numerous alternatives have been studied for inhibiting Aβ aggregation but, at this time, there are no effective treatments available. Here, we developed the tri-component nanohybrid system AuNPs@POM@PEG based on gold nanoparticles (AuNPs) covered with polyoxometalates (POMs) and polyethylene glycol (PEG). In this work, AuNPs@POM@PEG demonstrated the inhibition of the formation of amyloid fibrils, showing a 75% decrease in Aβ aggregation in vitro. As it is a potential candidate for the treatment of Alzheimer's disease, we evaluated the cytotoxicity of AuNPs@POM@PEG and its ability to cross the blood-brain barrier (BBB). We achieved a stable nanosystem that is non-cytotoxic below 2.5 nM to human neurovascular cells. The brain permeability of AuNPs@POM@PEG was analyzed in an in vitro microphysiological model of the BBB (BBB-on-a-chip), containing 3D human neurovascular cell co-cultures and microfluidics. The results show that AuNPs@POM@PEG was able to cross the brain endothelial barrier in the chip and demonstrated that POM does not affect the barrier integrity, giving the green light to further studies into this system as a nanotherapeutic.
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Affiliation(s)
- Marta Perxés Perich
- Catalan Institute of Nanoscience and Nanotechnology(ICN2) CSIC and BIST, Campus UAB, Bellaterra, 08193 Barcelona, Spain
- Nanobioengineering Group, Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
- Materials Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Sujey Palma-Florez
- Nanobioengineering Group, Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Clara Solé
- Nanobioengineering Group, Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Sara Goberna-Ferrón
- Catalan Institute of Nanoscience and Nanotechnology(ICN2) CSIC and BIST, Campus UAB, Bellaterra, 08193 Barcelona, Spain
- Instituto Universitario de Tecnología Química (CSIC-UPV), Universitat Politècnica de València, Avda. De los Naranjos s/n, 46022 Valencia, Spain
| | - Josep Samitier
- Nanobioengineering Group, Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials, and Nanomedicine (CIBER-BBN) Monforte de Lemos 3-5, Pabellón 11, 28029 Madrid, Spain
- Department of Electronics and Biomedical Engineering, University of Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Pedro Gómez-Romero
- Catalan Institute of Nanoscience and Nanotechnology(ICN2) CSIC and BIST, Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - Mònica Mir
- Nanobioengineering Group, Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials, and Nanomedicine (CIBER-BBN) Monforte de Lemos 3-5, Pabellón 11, 28029 Madrid, Spain
- Department of Electronics and Biomedical Engineering, University of Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Anna Lagunas
- Nanobioengineering Group, Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials, and Nanomedicine (CIBER-BBN) Monforte de Lemos 3-5, Pabellón 11, 28029 Madrid, Spain
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Jamuna NA, Kamalakshan A, Dandekar BR, Chittilappilly Devassy AM, Mondal J, Mandal S. Mechanistic Insight into the Amyloid Fibrillation Inhibition of Hen Egg White Lysozyme by Three Different Bile Acids. J Phys Chem B 2023; 127:2198-2213. [PMID: 36861956 DOI: 10.1021/acs.jpcb.3c00274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Amyloid aggregation of protein is linked to many neurodegenerative diseases. Identification of small molecules capable of targeting amyloidogenic proteins has gained significant importance. Introduction of hydrophobic and hydrogen bonding interactions through site-specific binding of small molecular ligand to protein can effectively modulate the protein aggregation pathway. Here, we investigate the possible roles of three different bile acids, cholic acid (CA), taurocholic acid (TCA), and lithocholic acid (LCA) with varying hydrophobic and hydrogen bonding properties in inhibiting protein fibrillation. Bile acids are an important class of steroid compounds that are synthesized in the liver from cholesterol. Increasing evidence suggests that altered taurine transport, cholesterol metabolism, and bile acid synthesis have strong implications in Alzheimer's disease. We find that the hydrophilic bile acids, CA and TCA (taurine conjugated form of CA), are substantially more efficient inhibitors of lysozyme fibrillation than the most hydrophobic secondary bile acid LCA. Although LCA binds more strongly with the protein and masks the Trp residues more prominently through hydrophobic interactions, the lesser extent of hydrogen bonding interactions at the active site has made LCA a relatively weaker inhibitor of HEWL aggregation than CA and TCA. The introduction of a greater number of hydrogen bonding channels by CA and TCA with several key amino acid residues which are prone to form oligomers and fibrils has weakened the protein's internal hydrogen bonding capabilities for undergoing amyloid aggregation.
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Affiliation(s)
- Nidhi Anilkumar Jamuna
- Department of Chemistry, National Institute of Technology, Tiruchirappalli, Tamil Nadu 620015, India
| | - Adithya Kamalakshan
- Department of Chemistry, National Institute of Technology, Tiruchirappalli, Tamil Nadu 620015, India
| | | | | | | | - Sarthak Mandal
- Department of Chemistry, National Institute of Technology, Tiruchirappalli, Tamil Nadu 620015, India
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Mura M, Humphreys B, Gilbert J, Salis A, Nylander T. Cation and buffer specific effects on the DNA-lipid interaction. Colloids Surf B Biointerfaces 2023; 223:113187. [PMID: 36739672 DOI: 10.1016/j.colsurfb.2023.113187] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/26/2023] [Accepted: 01/30/2023] [Indexed: 02/04/2023]
Abstract
Knowledge of DNA - lipid layer interactions is key for the development of biosensors, synthetic nanopores, scaffolds, and gene-delivery systems. These interactions are strongly affected by the ionic composition of the solvent. We have combined quartz crystal microbalance (QCM) and ellipsometry measurements to reveal how pH, buffers and alkali metal chloride salts affect the interaction of DNA with lipid bilayers (DOTAP/DOPC 30:70 in moles). We found that the thickness of the DNA layer adsorbed onto the lipid bilayer decreased in the order citrate > phosphate > Tris > HEPES. The effect of cations on the thickness of the DNA layer decreased in the order (K+ > Na+ > Cs+ ∼ Li+). Rationalization of the experimental results requires that adsorption, due to cation specific charge screening, is driven by the simultaneous action of two mechanisms namely, the law of matching water affinities for kosmotropes (Li+) and ion dispersion forces for chaotropes (Cs+). The outcome of these two opposing mechanisms is a "bell-shaped" specific cations sequence. Moreover, a superimposed buffer specificity, which goes beyond the simple effect of pH regulation, further modulated cation specificity. In summary, DNA-lipid bilayer interactions are maximized if citrate buffer (50 mM, pH 7.4) and KCl (100 mM) are used.
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Affiliation(s)
- Monica Mura
- Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden; Department of Chemical and Geological Sciences, University of Cagliari, Cittadella Universitaria, SS 554 bivio Sestu, 09042 Monserrato (CA), Italy; Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase (CSGI), Via della Lastruccia 3, Sesto Fiorentino (FI), I-50019, Italy
| | - Ben Humphreys
- Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Jennifer Gilbert
- Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Andrea Salis
- Department of Chemical and Geological Sciences, University of Cagliari, Cittadella Universitaria, SS 554 bivio Sestu, 09042 Monserrato (CA), Italy; Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase (CSGI), Via della Lastruccia 3, Sesto Fiorentino (FI), I-50019, Italy.
| | - Tommy Nylander
- Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden.
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7
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Effect of Antihypertensive Drug (Chlorothiazide) on Fibrillation of Lysozyme: A Combined Spectroscopy, Microscopy, and Computational Study. Int J Mol Sci 2023; 24:ijms24043112. [PMID: 36834523 PMCID: PMC9959601 DOI: 10.3390/ijms24043112] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/14/2023] [Accepted: 01/18/2023] [Indexed: 02/08/2023] Open
Abstract
Amyloid fibrils abnormally accumulate together in the human body under certain conditions, which can result in lethal conditions. Thus, blocking this aggregation may prevent or treat this disease. Chlorothiazide (CTZ) is a diuretic and is used to treat hypertension. Several previous studies suggest that diuretics prevent amyloid-related diseases and reduce amyloid aggregation. Thus, in this study we examine the effects of CTZ on hen egg white lysozyme (HEWL) aggregation using spectroscopic, docking, and microscopic approaches. Our results showed that under protein misfolding conditions of 55 °C, pH 2.0, and 600 rpm agitation, HEWL aggregated as evidenced by the increased turbidity and Rayleigh light scattering (RLS). Furthermore, thioflavin-T, as well as trans electron microscope (TEM) analysis confirmed the formation of amyloid structures. An anti-aggregation effect of CTZ is observed on HEWL aggregations. Circular dichroism (CD), TEM, and Thioflavin-T fluorescence show that both CTZ concentrations reduce the formation of amyloid fibrils as compared to fibrillated. The turbidity, RLS, and ANS fluorescence increase with CTZ increasing. This increase is attributed to the formation of a soluble aggregation. As evidenced by CD analysis, there was no significant difference in α-helix content and β-sheet content between at 10 µM CTZ and 100 µM. A TEM analysis of HEWL coincubated with CTZ at different concentrations validated all the above-mentioned results. The TEM results show that CTZ induces morphological changes in the typical structure of amyloid fibrils. The steady-state quenching study demonstrated that CTZ and HEWL bind spontaneously via hydrophobic interactions. HEWL-CTZ also interacts dynamically with changes in the environment surrounding tryptophan. Computational results revealed the binding of CTZ to ILE98, GLN57, ASP52, TRP108, TRP63, TRP63, ILE58, and ALA107 residues in HEWL via hydrophobic interactions and hydrogen bonds with a binding energy of -6.58 kcal mol-1. We suggest that at 10 µM and 100 μM, CTZ binds to the aggregation-prone region (APR) of HEWL and stabilizes it, thus preventing aggregation. Based on these findings, we can conclude that CTZ has antiamyloidogenic activity and can prevent fibril aggregation.
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Wawer J, Kaczkowska E, Karczewski J, Augustin-Nowacka D, Krakowiak J. Influence of stabilizing osmolytes on hen egg white lysozyme fibrillation. J Biomol Struct Dyn 2022; 40:13346-13353. [PMID: 34623219 DOI: 10.1080/07391102.2021.1984990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jarosław Wawer
- Department of Physical Chemistry, Faculty of Chemistry, Gdańsk University of Technology, Gdańsk, Poland
| | - Emilia Kaczkowska
- Department of Physical Chemistry, Faculty of Chemistry, Gdańsk University of Technology, Gdańsk, Poland
| | - Jakub Karczewski
- Institute of Nanotechnology and Materials Science, Faculty of Applied Physics and Mathematics, Gdańsk University of Technology, Gdańsk, Poland
| | | | - Joanna Krakowiak
- Department of Physical Chemistry, Faculty of Chemistry, Gdańsk University of Technology, Gdańsk, Poland
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BioMThermDB 1.0: Thermophysical Database of Proteins in Solutions. Int J Mol Sci 2022; 23:ijms232315371. [PMID: 36499696 PMCID: PMC9741033 DOI: 10.3390/ijms232315371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/01/2022] [Accepted: 12/03/2022] [Indexed: 12/12/2022] Open
Abstract
We present here a freely available web-based database, called BioMThermDB 1.0, of thermophysical and dynamic properties of various proteins and their aqueous solutions. It contains the hydrodynamic radius, electrophoretic mobility, zeta potential, self-diffusion coefficient, solution viscosity, and cloud-point temperature, as well as the conditions for those determinations and details of the experimental method. It can facilitate the meta-analysis and visualization of data, can enable comparisons, and may be useful for comparing theoretical model predictions with experiments.
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John T, Adler J, Elsner C, Petzold J, Krueger M, Martin LL, Huster D, Risselada HJ, Abel B. Mechanistic insights into the size-dependent effects of nanoparticles on inhibiting and accelerating amyloid fibril formation. J Colloid Interface Sci 2022; 622:804-818. [PMID: 35569410 DOI: 10.1016/j.jcis.2022.04.134] [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: 01/23/2022] [Revised: 04/05/2022] [Accepted: 04/23/2022] [Indexed: 10/18/2022]
Abstract
The aggregation of peptides into amyloid fibrils has been linked to ageing-related diseases, such as Alzheimer's and type 2 diabetes. Interfaces, particularly those with large nanostructured surfaces, can affect the kinetics of peptide aggregation, which ranges from complete inhibition to strong acceleration. While a number of physiochemical parameters determine interfacial effects, we focus here on the role of nanoparticle (NP) size and curvature. We used thioflavin T (ThT) fluorescence assays to demonstrate the size-dependent effects of NPs on amyloid fibril formation for the peptides Aβ40, NNFGAIL, GNNQQNY and VQIYVK. While 5 nm gold NPs (AuNP-5) retarded or inhibited the aggregation of all peptides except NNFGAIL, larger 20 nm gold NPs (AuNP-20) tended to accelerate or not influence peptide aggregation. Differences in the NP effects for the peptides resulted from the different peptide properties (size, tendency to aggregate) and associated surface binding affinities. Additional dynamic light scattering (DLS), electron microscopy, and atomic force microscopy (AFM) experiments with the Aβ40 peptide confirmed size-dependent NP effects on peptide aggregation, and also suggested a structural influence on the formed fibrils. NPs can serve as a surface for the adsorption of peptide monomers and enable nucleation to oligomers and fibril formation. However, molecular dynamics (MD) simulations showed that peptide oligomers were less stable at smaller NPs. High surface curvatures destabilized prefibrillar structures, which provides a possible explanation for inhibitory effects on fibril growth, provided that peptide-NP surface binding was relevant for fibril formation. These mechanistic insights can support the design of future nanostructured materials.
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Affiliation(s)
- Torsten John
- Leibniz Institute of Surface Engineering (IOM), Permoserstraße 15, 04318 Leipzig, Germany; Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry, Leipzig University, Linnéstraße 3, 04103 Leipzig, Germany; School of Chemistry, Monash University, Clayton, Victoria 3800, Australia
| | - Juliane Adler
- Institute for Medical Physics and Biophysics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany
| | - Christian Elsner
- Leibniz Institute of Surface Engineering (IOM), Permoserstraße 15, 04318 Leipzig, Germany
| | - Johannes Petzold
- Leibniz Institute of Surface Engineering (IOM), Permoserstraße 15, 04318 Leipzig, Germany
| | - Martin Krueger
- Institute of Anatomy, Leipzig University, Liebigstraße 13, 04103 Leipzig, Germany
| | - Lisandra L Martin
- School of Chemistry, Monash University, Clayton, Victoria 3800, Australia
| | - Daniel Huster
- Institute for Medical Physics and Biophysics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany
| | - Herre Jelger Risselada
- Leibniz Institute of Surface Engineering (IOM), Permoserstraße 15, 04318 Leipzig, Germany; Institute for Theoretical Physics, Georg-August-Universität Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany.
| | - Bernd Abel
- Leibniz Institute of Surface Engineering (IOM), Permoserstraße 15, 04318 Leipzig, Germany; Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry, Leipzig University, Linnéstraße 3, 04103 Leipzig, Germany.
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11
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Chen Y, Liu Q, Yang F, Yu H, Xie Y, Yao W. Submicron-size polystyrene modulates amyloid fibril formation: From the perspective of protein corona. Colloids Surf B Biointerfaces 2022; 218:112736. [DOI: 10.1016/j.colsurfb.2022.112736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 07/22/2022] [Accepted: 07/27/2022] [Indexed: 10/16/2022]
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12
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Effect of 1-Ethyl-3-methylimidazolium Tetrafluoroborate and Acetate Ionic Liquids on Stability and Amyloid Aggregation of Lysozyme. Int J Mol Sci 2022; 23:ijms23020783. [PMID: 35054967 PMCID: PMC8775716 DOI: 10.3390/ijms23020783] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/08/2022] [Accepted: 01/08/2022] [Indexed: 02/01/2023] Open
Abstract
Amyloid fibrils draw attention as potential novel biomaterials due to their high stability, strength, elasticity or resistance against degradation. Therefore, the controlled and fast fibrillization process is of great interest, which raises the demand for effective tools capable of regulating amyloid fibrillization. Ionic liquids (ILs) were identified as effective modulators of amyloid aggregation. The present work is focused on the study of the effect of 1-ethyl-3-methyl imidazolium-based ILs with kosmotropic anion acetate (EMIM-ac) and chaotropic cation tetrafluoroborate (EMIM-BF4) on the kinetics of lysozyme amyloid aggregation and morphology of formed fibrils using fluorescence and CD spectroscopy, differential scanning calorimetry, AFM with statistical image analysis and docking calculations. We have found that both ILs decrease the thermal stability of lysozyme and significantly accelerate amyloid fibrillization in a dose-dependent manner at concentrations of 0.5%, 1% and 5% (v/v) in conditions and time-frames when no fibrils are formed in ILs-free solvent. The effect of EMIM-BF4 is more prominent than EMIM-ac due to the different specific interactions of the anionic part with the protein surface. Although both ILs induced formation of amyloid fibrils with typical needle-like morphology, a higher variability of fibril morphology consisting of a different number of intertwining protofilaments was identified for EMIM-BF4.
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ZHANG C, NING Y, JIA Y, KANG M, HE Y, XU W, SHAH BR. Interaction investigation and phase transition of carrageenan/lysozyme complex system. FOOD SCIENCE AND TECHNOLOGY 2022. [DOI: 10.1590/fst.87222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
| | | | - Yin JIA
- Xinyang Normal University, China
| | | | - Yawen HE
- Xinyang Normal University, China
| | - Wei XU
- Xinyang Normal University, China
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Marchenkov V, Ryabova N, Balobanov V, Glukhov A, Ilyina N, Katina N. Under Conditions of Amyloid Formation Bovine Carbonic Anhydrase B Undergoes Fragmentation by Acid Hydrolysis. Biomolecules 2021; 11:1608. [PMID: 34827606 PMCID: PMC8615856 DOI: 10.3390/biom11111608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/23/2021] [Accepted: 10/28/2021] [Indexed: 11/23/2022] Open
Abstract
The development of many severe human diseases is associated with the formation of amyloid fibrils. Most of the available information on the process of amyloid formation has been obtained from studies of small proteins and peptides, wherein the features of complex proteins' aggregation remain insufficiently investigated. Our work aimed to research the amyloid aggregation of a large model protein, bovine carbonic anhydrase B (BCAB). It has previously been demonstrated that, when exposed to an acidic pH and elevated temperature, this protein forms amyloid fibrils. Here, we show that, under these conditions and before amyloid formation, BCAB undergoes fragmentation by acid hydrolysis to give free individual peptides and associated peptides. Fragments in associates contain a pronounced secondary structure and act as the main precursor of amyloid fibrils, wherein free peptides adopt mostly unstructured conformation and form predominantly irregular globular aggregates. Reduced acidity decreases the extent of acid hydrolysis, causing BCAB to form amorphous aggregates lacking the thioflavin T binding β-structure. The presented results provide new information on BCAB amyloid formation and show the importance of protein integrity control when working even in mildly acidic conditions.
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Affiliation(s)
| | | | | | | | - Nelly Ilyina
- Institute of Protein Research RAS, 142290 Pushchino, Russia
| | - Natalya Katina
- Institute of Protein Research RAS, 142290 Pushchino, Russia
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15
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Nirwal S, Bharathi V, Patel BK. Amyloid-like aggregation of bovine serum albumin at physiological temperature induced by cross-seeding effect of HEWL amyloid aggregates. Biophys Chem 2021; 278:106678. [PMID: 34492451 DOI: 10.1016/j.bpc.2021.106678] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 08/28/2021] [Accepted: 08/29/2021] [Indexed: 01/16/2023]
Abstract
BSA can form amyloid-like aggregates in vitro at 65 °C. Heterologous amyloid can proposedly cross-seed other protein's aggregation, however, general mechanisms and driving conditions remain to be vividly elucidated. Here, we examined if pre-formed HEWL amyloid can cross-seed the aggregation of BSA at physiological temperature, 37 °C, and whether the efficacy depends on the BSA conformation. We find that at pH 3.0, 37 °C where BSA manifests exposure of abundant hydrophobic patches, HEWL amyloid efficiently drives BSA into ThT-positive, sarkosyl-resistant, β-sheet rich amyloid-like aggregates exhibiting fibrils in TEM. On the contrary, HEWL amyloid fails to cross-seed the BSA aggregation at pH 7.0, 37 °C where BSA has largely internalized hydrophobic patches. Strikingly, human lysozyme amyloid could also cross-seed human serum albumin aggregation at pH 3.0, 37 °C. Thus, heterologous amyloid cross-seeding can help overcome the energy-barrier for aggregation of other proteins that, for any reason, may have perturbed and promiscuous structural conformation at physiological temperatures.
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Affiliation(s)
- Sadhana Nirwal
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Vidhya Bharathi
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Basant K Patel
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India.
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16
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The effect of macromolecular crowders on dielecric constant of aqueous electrolyte solutions. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Adam T, Dhahi TS, Gopinath SCB, Hashim U, Uda MNA. Recent advances in techniques for fabrication and characterization of nanogap biosensors: A review. Biotechnol Appl Biochem 2021; 69:1395-1417. [PMID: 34143905 DOI: 10.1002/bab.2212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 05/27/2021] [Indexed: 12/12/2022]
Abstract
Nanogap biosensors have fascinated researchers due to their excellent electrical properties. Nanogap biosensors comprise three arrays of electrodes that form nanometer-size gaps. The sensing gaps have become the major building blocks of several sensing applications, including bio- and chemosensors. One of the advantages of nanogap biosensors is that they can be fabricated in nanoscale size for various downstream applications. Several studies have been conducted on nanogap biosensors, and nanogap biosensors exhibit potential material properties. The possibilities of combining these unique properties with a nanoscale-gapped device and electrical detection systems allow excellent and potential prospects in biomolecular detection. However, their fabrication is challenging as the gap is becoming smaller. It includes high-cost, low-yield, and surface phenomena to move a step closer to the routine fabrications. This review summarizes different feasible techniques in the fabrication of nanogap electrodes, such as preparation by self-assembly with both conventional and nonconventional approaches. This review also presents a comprehensive analysis of the fabrication, potential applications, history, and the current status of nanogap biosensors with a special focus on nanogap-mediated bio- and chemical sonsors.
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Affiliation(s)
- Tijjani Adam
- Faculty of Electronic Engineering Technology, Universiti Malaysia Perlis, Kampus Uniciti Alam Sg. Chuchuh, Padang Besar (U), Perlis, Malaysia.,Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), Kangar, Perlis, 01000, Malaysia
| | - Th S Dhahi
- Physics Department, University of Basrah, Basra, Iraq.,Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), Kangar, Perlis, 01000, Malaysia
| | - Subash C B Gopinath
- Faculty of Chemical Engineering Technology, Universiti Malaysia Perlis (UniMAP), Arau, Perlis, 02600, Malaysia.,Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), Kangar, Perlis, 01000, Malaysia
| | - U Hashim
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), Kangar, Perlis, 01000, Malaysia
| | - M N A Uda
- Faculty of Chemical Engineering Technology, Universiti Malaysia Perlis (UniMAP), Arau, Perlis, 02600, Malaysia.,Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), Kangar, Perlis, 01000, Malaysia
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18
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Feng Z, Li Y, Bai Y. Elevated temperatures accelerate the formation of toxic amyloid fibrils of hen egg-white lysozyme. Vet Med Sci 2021; 7:1938-1947. [PMID: 33978313 PMCID: PMC8464291 DOI: 10.1002/vms3.522] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 03/17/2021] [Accepted: 04/22/2021] [Indexed: 11/17/2022] Open
Abstract
The formation of amyloid fibrils is critical for neurodegenerative diseases. Some physiochemical conditions can promote the conversion of proteins from soluble globular shapes into insoluble well‐organized amyloid fibrils. The aim of this study was to investigate the effect of temperatures on amyloid fibrils formation in vitro using the protein model of hen egg‐white lysozyme (HEWL). The HEWL fibrils were prepared at temperatures of 37, 45, 50 and 57°C in glycine solution of pH 2.2. Under transmission electron microscopy, we found the well‐organized HEWL amyloid fibrils at temperatures of 45, 50 and 57°C after 10 days of incubation. Thioflavin T and Congo red florescence assays confirmed that the formation and growth of HEWL fibrils displayed a temperature‐dependent increase, and 57°C produced the most amounts. Meanwhile, the surface hydrophobicity of aggregates was greatly increased by ANS binding assay, and β‐sheet contents by circular dichroism analysis were increased by 17.8%, 22.0% and 34.9%, respectively. Furthermore, the HEWL fibrils formed at 57°C caused significant cytotoxicity in SH‐SY5Y cells after 48 hr exposure, and the cell viability determined by MTT assay was decreased, with 81.35 ± 0.29% for 1 μM, 61.45 ± 2.62% for 2 μM, and 11.58 ± 0.39% (p < .01) for 3 μM. Nuclear staining results also confirmed the apoptosis features. These results suggest that the elevated temperatures could accelerate protein unfolding of the native structure and formation of toxic amyloid fibrils, which can improve understanding the mechanisms of the unfolding and misfolding process of prion protein.
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Affiliation(s)
- Zili Feng
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, P.R. China
| | - Ying Li
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, P.R. China
| | - Yu Bai
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, P.R. China
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19
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Kumar S, Kumar M, Tyagi YK, Kumar S. Inhibition of Amyloid Fibrillation of HEWL by 4-Methylcoumarin and 4-Methylthiocoumarin Derivatives. Curr Pharm Biotechnol 2021; 22:232-244. [PMID: 32933456 DOI: 10.2174/1389201021666200915112849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 03/28/2020] [Accepted: 07/30/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Several human diseases like Parkinson's, Alzheimer's disease, and systemic amyloidosis are associated with the misfolding and aggregation of protein molecules. OBJECTIVE The present study demonstrated the comparison of 4-methyl coumarin and 4-methylthiocoumarin derivative for their anti-amyloidogenic and disaggregation activities. The hen egg-white lysozyme is used as a model system to study protein aggregation and disaggregation under in vitro conditions. METHODS Techniques used in the study were Thioflavin T fluorescence assay, intrinsic fluorescence assay, circular dichroism, transmission electron microscopy, and molecular dynamics. RESULTS Fifteen compounds were screened for their anti-amyloidogenic and disaggregation potential. Six compounds significantly inhibited the fibril formation, whereas ten compounds showed disaggregation property of pre-formed fibrils. Under in vitro conditions, the compound C3 and C7 showed significant inhibition of fibril formation in a concentration-dependent manner as compared to control. C3 and C7 demonstrated 93% and 76% inhibition of fibril formation, respectively. Furthermore, C3 and C7 exhibited 83% and 76% disaggregation activity, respectively, of pre-formed HEWL fibrils at their highest concentration. These anti-amyloidogenic and disaggregation potential of C3 and C7 were validated by intrinsic fluorescence, CD, molecular dynamics, and TEM study. DISCUSSION 4-methylthiocoumarins derivatives have shown better anti-amyloidogenic activity as compared to 4-methylcoumarin derivatives for both amyloid formation as well as disaggregation of preformed amyloid fibrils. Structurally, the derivatives of 4-methylthiocoumarins (C3 and C7) contain thio group on 2nd position that might be responsible for anti-amyloidogenic activity as compared to 4- methylcoumarin derivatives (C2 and C4). CONCLUSION C3 and C7 are novel 4-methylthiocoumarin derivatives that can be used as a lead for alleviation and symptoms associated with protein aggregation disorders.
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Affiliation(s)
- Shivani Kumar
- University School of Biotechnology Guru Gobind Singh Indraprastha University Dwarka, Sector 16C, New Delhi- 110078, India
| | - Manoj Kumar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi-110029, India
| | - Yogesh K Tyagi
- University School of Basic and Applied Sciences Guru Gobind Singh Indraprastha University Dwarka, Sector 16C, New Delhi- 110078, India
| | - Suresh Kumar
- University School of Biotechnology Guru Gobind Singh Indraprastha University Dwarka, Sector 16C, New Delhi- 110078, India
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20
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Ermakova EA, Makshakova ON, Zuev YF, Sedov IA. Fibril fragments from the amyloid core of lysozyme: An accelerated molecular dynamics study. J Mol Graph Model 2021; 106:107917. [PMID: 33887522 DOI: 10.1016/j.jmgm.2021.107917] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 03/30/2021] [Accepted: 04/02/2021] [Indexed: 10/21/2022]
Abstract
Protein aggregation and formation of amyloid fibrils are associated with many diseases and present a ubiquitous problem in protein science. Hen egg white lysozyme (HEWL) can form fibrils both from the full length protein and from its fragments. In the present study, we simulated unfolding of the amyloidogenic fragment of HEWL encompassing residues 49-101 to study the conformational aspects of amyloidogenesis. The accelerated molecular dynamics approach was used to speed up the sampling of the fragment conformers under enhanced temperature. Analysis of conformational transformation and intermediate structures was performed. During the unfolding, the novel short-living and long-living β-structures are formed along with the unstructured random coils. Such β-structure enriched monomers can interact with each other and propagate into fibril-like forms. The stability of oligomers assembled from these monomers was evaluated in the course of MD simulations with explicit water. The residues playing a key role in fibril stabilization were determined. The work provides new insights into the processes occurring at the early stages of amyloid fibril assembly.
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Affiliation(s)
- Elena A Ermakova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, 420111, Kazan, Russia; Sirius University of Science and Technology, Olympic Ave, 1, 354340, Sochi, Russia.
| | - Olga N Makshakova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, 420111, Kazan, Russia; Sirius University of Science and Technology, Olympic Ave, 1, 354340, Sochi, Russia
| | - Yuriy F Zuev
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, 420111, Kazan, Russia
| | - Igor A Sedov
- Kazan Federal University, Kremlevskaya Str.,18, 420111, Kazan, Russia; Sirius University of Science and Technology, Olympic Ave, 1, 354340, Sochi, Russia
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21
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Brudar S, Hribar-Lee B. Effect of Buffer on Protein Stability in Aqueous Solutions: A Simple Protein Aggregation Model. J Phys Chem B 2021; 125:2504-2512. [PMID: 33656887 PMCID: PMC8041305 DOI: 10.1021/acs.jpcb.0c10339] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Liquid-liquid phase separation (LLPS) of proteins has recently been associated with the onset of numerous diseases. Despite several studies in this area of protein aggregation, buffer-specific effects always seem to be overlooked. In this study we investigated the influence of buffers on the phase stability of hen egg-white lysozyme (HEWL) and its respective protein-protein interactions by measuring the cloud point temperature, second virial coefficient, and interaction diffusion coefficient of several HEWL-buffer solutions (MOPS, phosphate, HEPES, cacodylate) at pH 7.0. The results indicate that the buffer molecules, depending on their hydration, adsorb on the protein surface, and modulate their electrostatic stability. The obtained information was used to extend the recently developed coarse-grained protein model to incorporate buffer-specific effects. Treated by Wertheim's perturbation theory the model qualitatively correctly predicted the experimentally observed phase separation of all investigated HEWL-buffer solutions, and further allowed us to predict the phase stability of protein formulations even in experimentally unattainable conditions. Since the theory can be straightforwardly extended to include multiple components it presents a useful tool to study protein aggregation in crowded cell-like systems.
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Affiliation(s)
- Sandi Brudar
- Faculty of Chemistry and Chemical Technology, University of Ljubljana,, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Barbara Hribar-Lee
- Faculty of Chemistry and Chemical Technology, University of Ljubljana,, Večna pot 113, SI-1000 Ljubljana, Slovenia
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22
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Simončič M, Lukšič M. Mechanistic differences in the effects of sucrose and sucralose on the phase stability of lysozyme solutions. J Mol Liq 2021; 326. [PMID: 35082450 DOI: 10.1016/j.molliq.2020.115245] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The effect of two disaccharide analogues, sucrose and sucralose, on the phase stability of aqueous lysozyme solutions has been addressed from a mechanistic viewpoint by a combination of experiment and molecular dynamics (MD) simulations. The influence of the added low molecular weight salts (NaBr, NaI and NaNO3) was considered as well. The cloud-point temperature measurements revealed a larger stabilizing effect of sucralose. Upon increasing sugar concentration, the protein solutions became more stable and differences in the effect of sucralose and sucrose amplified. It was confirmed that the addition of either of the two sugars imposed no secondary structure changes of the lysozyme. Enthalpies of lysozyme-sugar mixing were exothermic and a larger effect was recorded for sucralose. MD simulations indicated that acidic, basic and polar amino acid residues play predominant roles in the sugar-protein interactions, mainly through hydrogen bonding. Such sugar mediated protein-protein interactions are thought to be responsible for the biopreserative nature of sugars. Our observations hint at mechanistic differences in sugar-lysozyme interactions: while sucrose does not interact directly with the protein's surface for the most part (in line with the preferential hydration hypothesis), sucralose forms hydrogen bonds with acidic, basic and polar amino acid residues at the lysozyme's surface (in line with the water replacement hypothesis).
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Affiliation(s)
- Matjaž Simončič
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Miha Lukšič
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
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23
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On the Protein Fibrillation Pathway: Oligomer Intermediates Detection Using ATR-FTIR Spectroscopy. Molecules 2021; 26:molecules26040970. [PMID: 33673072 PMCID: PMC7918411 DOI: 10.3390/molecules26040970] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 02/02/2021] [Accepted: 02/05/2021] [Indexed: 01/17/2023] Open
Abstract
Oligomeric intermediates on the pathway of amyloid fibrillation are suspected as the main cytotoxins responsible for amyloid-related pathogenicity. As they appear to be a part of the lag phase of amyloid fibrillation when analyzed using standard methods such as Thioflavin T (ThT) fluorescence, a more sensitive method is needed for their detection. Here we apply Fourier transform infrared spectroscopy (FTIR) in attenuated total reflectance (ATR) mode for fast and cheap analysis of destabilized hen-egg-white lysozyme solution and detection of oligomer intermediates of amyloid fibrillation. Standard methods of protein aggregation analysis— Thioflavin T (ThT) fluorescence, atomic force microscopy (AFM), and 8-anilinonaphthalene-1-sulphonic acid (ANS) fluorescence were applied and compared to FTIR spectroscopy data. Results show the great potential of FTIR for both, qualitative and quantitative monitoring of oligomer formation based on the secondary structure changes. While oligomer intermediates do not induce significant changes in ThT fluorescence, their secondary structure changes were very prominent. Normalization of specific Amide I region peak intensities by using Amide II peak intensity as an internal standard provides an opportunity to use FTIR spectroscopy for both qualitative and quantitative analysis of biological samples and detection of potentially toxic oligomers, as well as for screening of efficiency of fibrillation procedures.
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24
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Prabakaran R, Rawat P, Thangakani AM, Kumar S, Gromiha MM. Protein aggregation: in silico algorithms and applications. Biophys Rev 2021; 13:71-89. [PMID: 33747245 PMCID: PMC7930180 DOI: 10.1007/s12551-021-00778-w] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 01/01/2021] [Indexed: 01/08/2023] Open
Abstract
Protein aggregation is a topic of immense interest to the scientific community due to its role in several neurodegenerative diseases/disorders and industrial importance. Several in silico techniques, tools, and algorithms have been developed to predict aggregation in proteins and understand the aggregation mechanisms. This review attempts to provide an essence of the vast developments in in silico approaches, resources available, and future perspectives. It reviews aggregation-related databases, mechanistic models (aggregation-prone region and aggregation propensity prediction), kinetic models (aggregation rate prediction), and molecular dynamics studies related to aggregation. With a multitude of prediction models related to aggregation already available to the scientific community, the field of protein aggregation is rapidly maturing to tackle new applications.
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Affiliation(s)
- R. Prabakaran
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai, Tamil Nadu India
| | - Puneet Rawat
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai, Tamil Nadu India
| | - A. Mary Thangakani
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai, Tamil Nadu India
| | - Sandeep Kumar
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT USA
| | - M. Michael Gromiha
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai, Tamil Nadu India
- School of Computing, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa Japan
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25
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Brudar S, Gujt J, Spohr E, Hribar-Lee B. Studying the mechanism of phase separation in aqueous solutions of globular proteins via molecular dynamics computer simulations. Phys Chem Chem Phys 2021; 23:415-424. [PMID: 33319872 PMCID: PMC8210815 DOI: 10.1039/d0cp05160h] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Proteins are the most abundant biomacromolecules in living cells, where they perform vital roles in virtually every biological process. To maintain their function, proteins need to remain in a stable (native) state. Inter- and intramolecular interactions in aqueous protein solutions govern the fate of proteins, as they can provoke their unfolding or association into aggregates. The initial steps of protein aggregation are difficult to capture experimentally, therefore we used molecular dynamics simulations in this study. We investigated the initial phase of aggregation of two different lysozymes, hen egg-white (HEWL) and T4 WT* lysozyme and also human lens γ-D crystallin by using atomistic simulations. We monitored the phase stability of their aqueous solutions by calculating time-dependent density fluctuations. We found that all proteins remained in their compact form despite aggregation. With an extensive analysis of intermolecular residue-residue interactions we discovered that arginine is of paramount importance in the initial stage of aggregation of HEWL and γ-D crystallin, meanwhile lysine was found to be the most involved amino acid in forming initial contacts between T4 WT* molecules.
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Affiliation(s)
- Sandi Brudar
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Večna pot 113, SI-1000 Ljubljana, Slovenia.
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26
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Rakshit S, Ghosh S, Roy R, Bhattacharya SC. Non-enzymatic electrochemical glucose sensing by Cu2O octahedrons: elucidating the protein adsorption signature. NEW J CHEM 2021. [DOI: 10.1039/d0nj04431h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Developing an electrochemical biosensor based on Cu2O octahedrons for rapid, sensitive and highly selective detection of glucose in real samples with an unprecedented analysis of their protein adsorption signature.
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Affiliation(s)
| | - Srabanti Ghosh
- Department of Chemical, Biological and Macromolecular Sciences
- S. N. Bose National Centre for Basic Sciences
- Kolkata 700 098
- India
| | - Rimi Roy
- Department of Chemistry
- Presidency University
- Kolkata 700 073
- India
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27
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Pignataro MF, Herrera MG, Dodero VI. Evaluation of Peptide/Protein Self-Assembly and Aggregation by Spectroscopic Methods. Molecules 2020; 25:E4854. [PMID: 33096797 PMCID: PMC7587993 DOI: 10.3390/molecules25204854] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/17/2020] [Accepted: 10/19/2020] [Indexed: 01/08/2023] Open
Abstract
The self-assembly of proteins is an essential process for a variety of cellular functions including cell respiration, mobility and division. On the other hand, protein or peptide misfolding and aggregation is related to the development of Parkinson's disease and Alzheimer's disease, among other aggregopathies. As a consequence, significant research efforts are directed towards the understanding of this process. In this review, we are focused on the use of UV-Visible Absorption Spectroscopy, Fluorescence Spectroscopy and Circular Dichroism to evaluate the self-organization of proteins and peptides in solution. These spectroscopic techniques are commonly available in most chemistry and biochemistry research laboratories, and together they are a powerful approach for initial as well as routine evaluation of protein and peptide self-assembly and aggregation under different environmental stimulus. Furthermore, these spectroscopic techniques are even suitable for studying complex systems like those in the food industry or pharmaceutical formulations, providing an overall idea of the folding, self-assembly, and aggregation processes, which is challenging to obtain with high-resolution methods. Here, we compiled and discussed selected examples, together with our results and those that helped us better to understand the process of protein and peptide aggregation. We put particular emphasis on the basic description of the methods as well as on the experimental considerations needed to obtain meaningful information, to help those who are just getting into this exciting area of research. Moreover, this review is particularly useful to those out of the field who would like to improve reproducibility in their cellular and biomedical experiments, especially while working with peptide and protein systems as an external stimulus. Our final aim is to show the power of these low-resolution techniques to improve our understanding of the self-assembly of peptides and proteins and translate this fundamental knowledge in biomedical research or food applications.
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Affiliation(s)
- María Florencia Pignataro
- Department of Physiology and Molecular and Cellular Biology, Institute of Biosciences, Biotechnology and Translational Biology (iB3), Faculty of Exact and Natural Sciences, University of Buenos Aires, Buenos Aires C1428EG, Argentina;
- Institute of Biological Chemistry and Physical Chemistry, Dr. Alejandro Paladini, University of Buenos Aires-CONICET, Buenos Aires C1113AAD, Argentina
| | - María Georgina Herrera
- Department of Physiology and Molecular and Cellular Biology, Institute of Biosciences, Biotechnology and Translational Biology (iB3), Faculty of Exact and Natural Sciences, University of Buenos Aires, Buenos Aires C1428EG, Argentina;
- Institute of Biological Chemistry and Physical Chemistry, Dr. Alejandro Paladini, University of Buenos Aires-CONICET, Buenos Aires C1113AAD, Argentina
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, 33615 Bielefeld, Germany
| | - Verónica Isabel Dodero
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, 33615 Bielefeld, Germany
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28
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Bag S, Rauwolf S, Suyetin M, Schwaminger SP, Wenzel W, Berensmeier S. Buffer Influence on the Amino Acid Silica Interaction. Chemphyschem 2020; 21:2347-2356. [PMID: 32794279 PMCID: PMC7702087 DOI: 10.1002/cphc.202000572] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 08/11/2020] [Indexed: 12/11/2022]
Abstract
Protein-surface interactions are exploited in various processes in life sciences and biotechnology. Many of such processes are performed in presence of a buffer system, which is generally believed to have an influence on the protein-surface interaction but is rarely investigated systematically. Combining experimental and theoretical methodologies, we herein demonstrate the strong influence of the buffer type on protein-surface interactions. Using state of the art chromatographic experiments, we measure the interaction between individual amino acids and silica, as a reference to understand protein-surface interactions. Among all the 20 proteinogenic amino acids studied, we found that arginine (R) and lysine (K) bind most strongly to silica, a finding validated by free energy calculations. We further measured the binding of R and K at different pH in presence of two different buffers, MOPS (3-(N-morpholino)propanesulfonic acid) and TRIS (tris(hydroxymethyl)aminomethane), and find dramatically different behavior. In presence of TRIS, the binding affinity of R/K increases with pH, whereas we observe an opposite trend for MOPS. These results can be understood using a multiscale modelling framework combining molecular dynamics simulation and Langmuir adsorption model. The modelling approach helps to optimize buffer conditions in various fields like biosensors, drug delivery or bio separation engineering prior to the experiment.
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Affiliation(s)
- Saientan Bag
- Institute of Nanotechnology (INT)Karlsruhe Institute of Technology (KIT)KarlsruheGermany
| | - Stefan Rauwolf
- Bioseparation Engineering GroupDepartment of Mechanical EngineeringTechnical University of Munich(TUM)GarchingGermany
| | - Mikhail Suyetin
- Institute of Nanotechnology (INT)Karlsruhe Institute of Technology (KIT)KarlsruheGermany
| | - Sebastian P. Schwaminger
- Bioseparation Engineering GroupDepartment of Mechanical EngineeringTechnical University of Munich(TUM)GarchingGermany
| | - Wolfgang Wenzel
- Institute of Nanotechnology (INT)Karlsruhe Institute of Technology (KIT)KarlsruheGermany
| | - Sonja Berensmeier
- Bioseparation Engineering GroupDepartment of Mechanical EngineeringTechnical University of Munich(TUM)GarchingGermany
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Amirkulova DB, Chakraborty M, White AD. Experimentally Consistent Simulation of Aβ 21-30 Peptides with a Minimal NMR Bias. J Phys Chem B 2020; 124:8266-8277. [PMID: 32845146 DOI: 10.1021/acs.jpcb.0c07129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Misfolded amyloid peptides are neurotoxic molecules associated with Alzheimer's disease. The Aβ21-30 peptide fragment is a decapeptide fragment of the complete Aβ42 peptide which is a hypothesized cause of Alzheimer's disease via amyloid fibrillogenesis. Aβ21-30 is investigated here with a combination of NMR (nuclear magnetic resonance) spectroscopy experiments and molecular dynamics simulations with experiment directed simulation (EDS). EDS is a maximum entropy biasing method that augments a molecular dynamics simulation with experimental data (NMR chemical shifts) to improve agreement with experiments and thus accuracy. EDS molecular dynamics shows that the Aβ21-30 monomer has a β turn stabilized by the following interactions: S26-K28, D23-S26, and D23-K28. NMR, total correlation spectroscopy, and rotating frame Overhauser effect spectroscopy experiments provide independent agreement. Subsequent two- and four-monomer EDS simulations show aggregation. Diffusion coefficients calculated from molecular simulation also agreed with experimentally measured values only after using EDS, providing independent assessment of accuracy. This work demonstrates how accuracy can be improved by directly using experimental data in molecular dynamics of complex processes like self-assembly.
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Affiliation(s)
- Dilnoza B Amirkulova
- Department of Chemical Engineering, University of Rochester, Rochester, New York 14627, United States
| | - Maghesree Chakraborty
- Department of Chemical Engineering, University of Rochester, Rochester, New York 14627, United States
| | - Andrew D White
- Department of Chemical Engineering, University of Rochester, Rochester, New York 14627, United States
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Salis A, Cappai L, Carucci C, Parsons DF, Monduzzi M. Specific Buffer Effects on the Intermolecular Interactions among Protein Molecules at Physiological pH. J Phys Chem Lett 2020; 11:6805-6811. [PMID: 32787211 DOI: 10.1021/acs.jpclett.0c01900] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
BSA and lysozyme molecular motion at pH 7.15 is buffer-specific. Adsorption of buffer ions on protein surfaces modulates the protein surface charge and thus protein-protein interactions. Interactions were estimated by means of the interaction parameter kD obtained from plots of diffusion coefficients at different protein concentrations (Dapp = D0[1 + kDCprotein]) via dynamic light scattering and nuclear magnetic resonance. The obtained results agree with recent findings confirming doubts regarding the validity of the Henderson-Hasselbalch equation, which has traditionally provided a basis for understanding pH buffers of primary importance in solution chemistry, electrochemistry, and biochemistry.
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Affiliation(s)
- Andrea Salis
- Department of Chemical and Geological Sciences, University of Cagliari, and Centro NanoBiotecnologie Sardegna (CNBS), Cittadella Universitaria, SS 554 bivio Sestu, 09042 Monserrato (CA), Italy
- Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase (CSGI), Florence, Italy
- Unità Operativa University of Cagliari, Cagliari, Italy
| | - Luca Cappai
- Department of Chemical and Geological Sciences, University of Cagliari, and Centro NanoBiotecnologie Sardegna (CNBS), Cittadella Universitaria, SS 554 bivio Sestu, 09042 Monserrato (CA), Italy
| | - Cristina Carucci
- Department of Chemical and Geological Sciences, University of Cagliari, and Centro NanoBiotecnologie Sardegna (CNBS), Cittadella Universitaria, SS 554 bivio Sestu, 09042 Monserrato (CA), Italy
- Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase (CSGI), Florence, Italy
- Unità Operativa University of Cagliari, Cagliari, Italy
| | - Drew F Parsons
- Discipline of Chemistry and Physics, College of Science, Health, Engineering & Education, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
| | - Maura Monduzzi
- Department of Chemical and Geological Sciences, University of Cagliari, and Centro NanoBiotecnologie Sardegna (CNBS), Cittadella Universitaria, SS 554 bivio Sestu, 09042 Monserrato (CA), Italy
- Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase (CSGI), Florence, Italy
- Unità Operativa University of Cagliari, Cagliari, Italy
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31
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do Amaral MJ, Araujo TS, Díaz NC, Accornero F, Polycarpo CR, Cordeiro Y, Cabral KM, Almeida MS. Phase Separation and Disorder-to-Order Transition of Human Brain Expressed X-Linked 3 (hBEX3) in the Presence of Small Fragments of tRNA. J Mol Biol 2020; 432:2319-2348. [DOI: 10.1016/j.jmb.2020.02.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 02/10/2020] [Accepted: 02/27/2020] [Indexed: 12/19/2022]
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32
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John T, Dealey TJA, Gray NP, Patil NA, Hossain MA, Abel B, Carver JA, Hong Y, Martin LL. The Kinetics of Amyloid Fibrillar Aggregation of Uperin 3.5 Is Directed by the Peptide’s Secondary Structure. Biochemistry 2019; 58:3656-3668. [DOI: 10.1021/acs.biochem.9b00536] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Torsten John
- School of Chemistry, Monash University, Clayton, Victoria 3800, Australia
- Leibniz Institute of Surface Engineering (IOM), Permoserstraße 15, 04318 Leipzig, Germany
- Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry, Leipzig University, Linnéstraße 3, 04103 Leipzig, Germany
| | - Tiara J. A. Dealey
- School of Chemistry, Monash University, Clayton, Victoria 3800, Australia
| | - Nicholas P. Gray
- School of Chemistry, Monash University, Clayton, Victoria 3800, Australia
| | - Nitin A. Patil
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Mohammed A. Hossain
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Bernd Abel
- Leibniz Institute of Surface Engineering (IOM), Permoserstraße 15, 04318 Leipzig, Germany
- Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry, Leipzig University, Linnéstraße 3, 04103 Leipzig, Germany
| | - John A. Carver
- Research School of Chemistry, The Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - Yuning Hong
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Lisandra L. Martin
- School of Chemistry, Monash University, Clayton, Victoria 3800, Australia
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Varma N, Kukrety H, Ravi VK, Kumar S. Bacopa monnieriinhibit hen egg white lysozyme fibrillation and help in retaining its activity at acidic condition. J Biomol Struct Dyn 2019; 38:1786-1797. [DOI: 10.1080/07391102.2019.1617784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Neelakant Varma
- Laboratory of Forensic Biology and Biotechnology, Institute of Forensic Science, Gujarat Forensic Sciences University, Gandhinagar, Gujarat, India
| | - Himanshi Kukrety
- Laboratory of Forensic Biology and Biotechnology, Institute of Forensic Science, Gujarat Forensic Sciences University, Gandhinagar, Gujarat, India
| | - Vijay K. Ravi
- School of Chemical and Biotechnology, SASTRA University, Thanjavur, India
| | - Satish Kumar
- Laboratory of Forensic Biology and Biotechnology, Institute of Forensic Science, Gujarat Forensic Sciences University, Gandhinagar, Gujarat, India
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