1
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Olgenblum GI, Hutcheson BO, Pielak GJ, Harries D. Protecting Proteins from Desiccation Stress Using Molecular Glasses and Gels. Chem Rev 2024; 124:5668-5694. [PMID: 38635951 PMCID: PMC11082905 DOI: 10.1021/acs.chemrev.3c00752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 02/18/2024] [Accepted: 02/22/2024] [Indexed: 04/20/2024]
Abstract
Faced with desiccation stress, many organisms deploy strategies to maintain the integrity of their cellular components. Amorphous glassy media composed of small molecular solutes or protein gels present general strategies for protecting against drying. We review these strategies and the proposed molecular mechanisms to explain protein protection in a vitreous matrix under conditions of low hydration. We also describe efforts to exploit similar strategies in technological applications for protecting proteins in dry or highly desiccated states. Finally, we outline open questions and possibilities for future explorations.
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Affiliation(s)
- Gil I. Olgenblum
- Institute
of Chemistry, Fritz Haber Research Center, and The Harvey M. Krueger
Family Center for Nanoscience & Nanotechnology, The Hebrew University, Jerusalem 9190401, Israel
| | - Brent O. Hutcheson
- Department
of Chemistry, University of North Carolina
at Chapel Hill (UNC-CH), Chapel
Hill, North Carolina 27599, United States
| | - Gary J. Pielak
- Department
of Chemistry, University of North Carolina
at Chapel Hill (UNC-CH), Chapel
Hill, North Carolina 27599, United States
- Department
of Chemistry, Department of Biochemistry & Biophysics, Integrated
Program for Biological & Genome Sciences, Lineberger Comprehensive
Cancer Center, University of North Carolina
at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Daniel Harries
- Institute
of Chemistry, Fritz Haber Research Center, and The Harvey M. Krueger
Family Center for Nanoscience & Nanotechnology, The Hebrew University, Jerusalem 9190401, Israel
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2
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Garfagnini T, Bemporad F, Harries D, Chiti F, Friedler A. Amyloid Aggregation Is Potently Slowed Down by Osmolytes Due to Compaction of Partially Folded State. J Mol Biol 2023; 435:168281. [PMID: 37734431 DOI: 10.1016/j.jmb.2023.168281] [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: 03/25/2023] [Revised: 07/30/2023] [Accepted: 09/11/2023] [Indexed: 09/23/2023]
Abstract
Amyloid aggregation is a key process in amyloidoses and neurodegenerative diseases. Hydrophobicity is one of the major driving forces for this type of aggregation, as an increase in hydrophobicity generally correlates with aggregation susceptibility and rate. However, most experimental systems in vitro and prediction tools in silico neglect the contribution of protective osmolytes present in the cellular environment. Here, we assessed the role of hydrophobic mutations in amyloid aggregation in the presence of osmolytes. To achieve this goal, we used the model protein human muscle acylphosphatase (mAcP) and mutations to leucine that increased its hydrophobicity without affecting its thermodynamic stability. Osmolytes significantly slowed down the aggregation kinetics of the hydrophobic mutants, with an effect larger than that observed on the wild-type protein. The effect increased as the mutation site was closer to the middle of the protein sequence. We propose that the preferential exclusion of osmolytes from mutation-introduced hydrophobic side-chains quenches the aggregation potential of the ensemble of partially unfolded states of the protein by inducing its compaction and inhibiting its self-assembly with other proteins. Our results suggest that including the effect of the cellular environment in experimental setups and predictive softwares, for both mechanistic studies and drug design, is essential in order to obtain a more complete combination of the driving forces of amyloid aggregation.
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Affiliation(s)
- Tommaso Garfagnini
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 9190401, Israel
| | - Francesco Bemporad
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence 50134, Italy
| | - Daniel Harries
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 9190401, Israel; The Fritz Haber Research Center, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 9190401, Israel
| | - Fabrizio Chiti
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence 50134, Italy
| | - Assaf Friedler
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 9190401, Israel.
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3
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Olgenblum GI, Carmon N, Harries D. Not Always Sticky: Specificity of Protein Stabilization by Sugars Is Conferred by Protein-Water Hydrogen Bonds. J Am Chem Soc 2023; 145:23308-23320. [PMID: 37845197 PMCID: PMC10603812 DOI: 10.1021/jacs.3c08702] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
Solutes added to buffered solutions directly impact protein folding. Protein stabilization by cosolutes or crowders has been shown to be largely driven by protein-cosolute volume exclusion complemented by chemical and soft interactions. By contrast to previous studies that indicate the invariably destabilizing role of soft protein-sugar attractions, we show here that soft interactions with sugar cosolutes are protein-specific and can be stabilizing or destabilizing. We experimentally follow the folding of two model miniproteins that are only marginally stable but in the presence of sugars and polyols fold into representative and distinct secondary structures: β-hairpin or α-helix. Our mean-field model reveals that while protein-sugar excluded volume interactions have a similar stabilizing effect on both proteins, the soft interactions add a destabilizing contribution to one miniprotein but further stabilize the other. Using molecular dynamics simulations, we link the soft protein-cosolute interactions to the weakening of direct protein-water hydrogen bonding due to the presence of sugars. Although these weakened hydrogen bonds destabilize both the native and denatured states of the two proteins, the resulting contribution to the folding free energy can be positive or negative depending on the amino acid sequence. This study indicates that the significant variation between proteins in their soft interactions with sugar determines the specific response of different proteins, even to the same sugar.
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Affiliation(s)
- Gil I Olgenblum
- The Fritz Haber Research Center, and the Harvey M. Kruger Center for Nanoscience & Nanotechnology, Institute of Chemistry, The Hebrew University, Jerusalem 9190401, Israel
| | - Neta Carmon
- The Fritz Haber Research Center, and the Harvey M. Kruger Center for Nanoscience & Nanotechnology, Institute of Chemistry, The Hebrew University, Jerusalem 9190401, Israel
| | - Daniel Harries
- The Fritz Haber Research Center, and the Harvey M. Kruger Center for Nanoscience & Nanotechnology, Institute of Chemistry, The Hebrew University, Jerusalem 9190401, Israel
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4
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Stewart CJ, Olgenblum GI, Propst A, Harries D, Pielak GJ. Resolving the enthalpy of protein stabilization by macromolecular crowding. Protein Sci 2023; 32:e4573. [PMID: 36691735 PMCID: PMC9942490 DOI: 10.1002/pro.4573] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 01/11/2023] [Accepted: 01/13/2023] [Indexed: 01/25/2023]
Abstract
Proteins in the cellular milieu reside in environments crowded by macromolecules and other solutes. Although crowding can significantly impact the protein folded state stability, most experiments are conducted in dilute buffered solutions. To resolve the effect of crowding on protein stability, we use 19 F nuclear magnetic resonance spectroscopy to follow the reversible, two-state unfolding thermodynamics of the N-terminal Src homology 3 domain of the Drosophila signal transduction protein drk in the presence of polyethylene glycols (PEGs) of various molecular weights and concentrations. Contrary to most current theories of crowding that emphasize steric protein-crowder interactions as the main driving force for entropically favored stabilization, our experiments show that PEG stabilization is accompanied by significant heat release, and entropy disfavors folding. Using our newly developed model, we find that stabilization by ethylene glycol and small PEGs is driven by favorable binding to the folded state. In contrast, for larger PEGs, chemical or soft PEG-protein interactions do not play a significant role. Instead, folding is favored by excluded volume PEG-protein interactions and an exothermic nonideal mixing contribution from release of confined PEG and water upon folding. Our results indicate that crowding acts through molecular interactions subtler than previously assumed and that interactions between solution components with both the folded and unfolded states must be carefully considered.
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Affiliation(s)
- Claire J. Stewart
- Department of ChemistryUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Gil I. Olgenblum
- Institute of Chemistry & the Fritz Haber Research Center, The Hebrew UniversityJerusalemIsrael
| | - Ashlee Propst
- Department of ChemistryUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Daniel Harries
- Institute of Chemistry & the Fritz Haber Research Center, The Hebrew UniversityJerusalemIsrael
| | - Gary J. Pielak
- Department of ChemistryUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
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5
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Housmans JAJ, Wu G, Schymkowitz J, Rousseau F. A guide to studying protein aggregation. FEBS J 2023; 290:554-583. [PMID: 34862849 DOI: 10.1111/febs.16312] [Citation(s) in RCA: 53] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/18/2021] [Accepted: 12/03/2021] [Indexed: 02/04/2023]
Abstract
Disrupted protein folding or decreased protein stability can lead to the accumulation of (partially) un- or misfolded proteins, which ultimately cause the formation of protein aggregates. Much of the interest in protein aggregation is associated with its involvement in a wide range of human diseases and the challenges it poses for large-scale biopharmaceutical manufacturing and formulation of therapeutic proteins and peptides. On the other hand, protein aggregates can also be functional, as observed in nature, which triggered its use in the development of biomaterials or therapeutics as well as for the improvement of food characteristics. Thus, unmasking the various steps involved in protein aggregation is critical to obtain a better understanding of the underlying mechanism of amyloid formation. This knowledge will allow a more tailored development of diagnostic methods and treatments for amyloid-associated diseases, as well as applications in the fields of new (bio)materials, food technology and therapeutics. However, the complex and dynamic nature of the aggregation process makes the study of protein aggregation challenging. To provide guidance on how to analyse protein aggregation, in this review we summarize the most commonly investigated aspects of protein aggregation with some popular corresponding methods.
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Affiliation(s)
- Joëlle A J Housmans
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Guiqin Wu
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Frederic Rousseau
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
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6
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Quinn SD, Dresser L, Graham S, Conteduca D, Shepherd J, Leake MC. Crowding-induced morphological changes in synthetic lipid vesicles determined using smFRET. Front Bioeng Biotechnol 2022; 10:958026. [PMID: 36394015 PMCID: PMC9650091 DOI: 10.3389/fbioe.2022.958026] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 10/13/2022] [Indexed: 12/02/2022] Open
Abstract
Lipid vesicles are valuable mesoscale molecular confinement vessels for studying membrane mechanics and lipid–protein interactions, and they have found utility among bio-inspired technologies, including drug delivery vehicles. While vesicle morphology can be modified by changing the lipid composition and introducing fusion or pore-forming proteins and detergents, the influence of extramembrane crowding on vesicle morphology has remained under-explored owing to a lack of experimental tools capable of capturing morphological changes on the nanoscale. Here, we use biocompatible polymers to simulate molecular crowding in vitro, and through combinations of FRET spectroscopy, lifetime analysis, dynamic light scattering, and single-vesicle imaging, we characterize how crowding regulates vesicle morphology. We show that both freely diffusing and surface-tethered vesicles fluorescently tagged with the DiI and DiD FRET pair undergo compaction in response to modest concentrations of sorbitol, polyethylene glycol, and Ficoll. A striking observation is that sorbitol results in irreversible compaction, whereas the influence of high molecular weight PEG-based crowders was found to be reversible. Regulation of molecular crowding allows for precise control of the vesicle architecture in vitro, with vast implications for drug delivery and vesicle trafficking systems. Furthermore, our observations of vesicle compaction may also serve to act as a mechanosensitive readout of extramembrane crowding.
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Affiliation(s)
- Steven D. Quinn
- School of Physics, Engineering and Technology, University of York, York, United Kingdom
- York Biomedical Research Institute, University of York, York, United Kingdom
| | - Lara Dresser
- School of Physics, Engineering and Technology, University of York, York, United Kingdom
| | - Sarah Graham
- School of Physics, Engineering and Technology, University of York, York, United Kingdom
| | - Donato Conteduca
- School of Physics, Engineering and Technology, University of York, York, United Kingdom
| | - Jack Shepherd
- School of Physics, Engineering and Technology, University of York, York, United Kingdom
- Department of Biology, University of York, York, United Kingdom
| | - Mark C. Leake
- School of Physics, Engineering and Technology, University of York, York, United Kingdom
- York Biomedical Research Institute, University of York, York, United Kingdom
- Department of Biology, University of York, York, United Kingdom
- *Correspondence: Mark C. Leake,
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7
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Gorensek-Benitez AH, Kirk B, Myers JK. Protein Fibrillation under Crowded Conditions. Biomolecules 2022; 12:biom12070950. [PMID: 35883507 PMCID: PMC9312947 DOI: 10.3390/biom12070950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/01/2022] [Accepted: 07/03/2022] [Indexed: 12/04/2022] Open
Abstract
Protein amyloid fibrils have widespread implications for human health. Over the last twenty years, fibrillation has been studied using a variety of crowding agents to mimic the packed interior of cells or to probe the mechanisms and pathways of the process. We tabulate and review these results by considering three classes of crowding agent: synthetic polymers, osmolytes and other small molecules, and globular proteins. While some patterns are observable for certain crowding agents, the results are highly variable and often depend on the specific pairing of crowder and fibrillating protein.
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Affiliation(s)
- Annelise H. Gorensek-Benitez
- Department of Chemistry and Biochemistry, Colorado College, Colorado Springs, CO 80903, USA
- Correspondence: (A.H.G.-B.); (J.K.M.)
| | - Bryan Kirk
- Department of Biology, Davidson College, Davidson, NC 28035, USA;
| | - Jeffrey K. Myers
- Department of Chemistry, Davidson College, Davidson, NC 28035, USA
- Correspondence: (A.H.G.-B.); (J.K.M.)
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8
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Speer SL, Stewart CJ, Sapir L, Harries D, Pielak GJ. Macromolecular Crowding Is More than Hard-Core Repulsions. Annu Rev Biophys 2022; 51:267-300. [PMID: 35239418 DOI: 10.1146/annurev-biophys-091321-071829] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cells are crowded, but proteins are almost always studied in dilute aqueous buffer. We review the experimental evidence that crowding affects the equilibrium thermodynamics of protein stability and protein association and discuss the theories employed to explain these observations. In doing so, we highlight differences between synthetic polymers and biologically relevant crowders. Theories based on hard-core interactions predict only crowding-induced entropic stabilization. However, experiment-based efforts conducted under physiologically relevant conditions show that crowding can destabilize proteins and their complexes. Furthermore, quantification of the temperature dependence of crowding effects produced by both large and small cosolutes, including osmolytes, sugars, synthetic polymers, and proteins, reveals enthalpic effects that stabilize or destabilize proteins. Crowding-induced destabilization and the enthalpic component point to the role of chemical interactions between and among the macromolecules, cosolutes, and water. We conclude with suggestions for future studies. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Shannon L Speer
- Department of Chemistry, University of North Carolina at Chapel Hill, North Carolina, USA;
| | - Claire J Stewart
- Department of Chemistry, University of North Carolina at Chapel Hill, North Carolina, USA;
| | - Liel Sapir
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina, USA
| | - Daniel Harries
- Institute of Chemistry and The Fritz Haber Research Center, The Hebrew University, Jerusalem, Israel
| | - Gary J Pielak
- Department of Chemistry, University of North Carolina at Chapel Hill, North Carolina, USA; .,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, North Carolina, USA.,Lineberger Cancer Research Center, University of North Carolina at Chapel Hill, North Carolina, USA
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9
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Ghosh S, Saurabh A, Prabhu NP. Spectroscopic studies on the stability and nucleation-independent fibrillation of partially-unfolded proteins in crowded environment. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 264:120307. [PMID: 34461523 DOI: 10.1016/j.saa.2021.120307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 07/30/2021] [Accepted: 08/17/2021] [Indexed: 06/13/2023]
Abstract
Fibril formation of globular proteins is driven by attaining an appropriate partially-unfolded conformation. Excluded volume effect exerted by the presence of other macromolecules in the solution, as found in the cellular interior, might affect the conformational state of proteins and alter their fibril formation process. The change in structure, stability and rate of fibril formation of aggregation-prone partially-unfolded states of lysozyme (Lyz) and α-lactalbumin (ALA) in the presence of different sizes of polyethylene glycol (PEG) is examined using spectroscopic methods. Thermal denaturation and far-UV CD studies suggest that Lyz is stabilized by PEGs and the stability increases with increasing concentration of PEGs. However, the stability of ALA depends on the size and concentration of PEG. The change in enthalpy of unfolding indicates the existence of soft-interactions between the proteins and PEG along with excluded volume effect. Fibrillation rate of Lyz is not significantly altered in the presence of lower concentrations of PEGs suggesting that the crowding effect dominates the viscosity-induced retardation of protein association whereas at higher concentrations the rates are reduced. In case of ALA, the rate of fibrillation is drastically reduced; however, there is a marginal increase with the increasing concentration of PEG. The results suggest that the fibril formation is influenced by change in initial conformation of the partially-unfolded states of the proteins and their stability in the presence of the crowding agent. Further, the size and concentration of the crowding agent, and the soft-interaction between the proteins and PEG also affects the fibrillation.
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Affiliation(s)
- Subhasree Ghosh
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, India
| | - Archi Saurabh
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, India
| | - N Prakash Prabhu
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, India.
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10
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Hakala T, Yates EV, Challa PK, Toprakcioglu Z, Nadendla K, Matak-Vinkovic D, Dobson CM, Martínez R, Corzana F, Knowles TPJ, Bernardes GJL. Accelerating Reaction Rates of Biomolecules by Using Shear Stress in Artificial Capillary Systems. J Am Chem Soc 2021; 143:16401-16410. [PMID: 34606279 PMCID: PMC8517977 DOI: 10.1021/jacs.1c03681] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Indexed: 12/15/2022]
Abstract
Biomimetics is a design principle within chemistry, biology, and engineering, but chemistry biomimetic approaches have been generally limited to emulating nature's chemical toolkit while emulation of nature's physical toolkit has remained largely unexplored. To begin to explore this, we designed biophysically mimetic microfluidic reactors with characteristic length scales and shear stresses observed within capillaries. We modeled the effect of shear with molecular dynamics studies and showed that this induces specific normally buried residues to become solvent accessible. We then showed using kinetics experiments that rates of reaction of these specific residues in fact increase in a shear-dependent fashion. We applied our results in the creation of a new microfluidic approach for the multidimensional study of cysteine biomarkers. Finally, we used our approach to establish dissociation of the therapeutic antibody trastuzumab in a reducing environment. Our results have implications for the efficacy of existing therapeutic antibodies in blood plasma as well as suggesting in general that biophysically mimetic chemistry is exploited in biology and should be explored as a research area.
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Affiliation(s)
- Tuuli
A. Hakala
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Emma V. Yates
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Pavan K. Challa
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Zenon Toprakcioglu
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Karthik Nadendla
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Dijana Matak-Vinkovic
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Christopher M. Dobson
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Rodrigo Martínez
- Departamento
de Química, Universidad de La Rioja, 26006 Logroño, Spain
| | - Francisco Corzana
- Departamento
de Química, Centro de Investigación en Síntesis
Química, Universidad de La Rioja, 26006 Logroño, Spain
| | - Tuomas P. J. Knowles
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- Cavendish
Laboratory, University of Cambridge, J. J. Thomson Avenue, CB3 0HE Cambridge, United Kingdom
| | - Gonçalo J. L. Bernardes
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina de Universidad de Lisboa, Avenida Prof. Egas Moniz, 1649-028 Lisboa, Portugal
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11
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Olgenblum GI, Wien F, Sapir L, Harries D. β-Hairpin Miniprotein Stabilization in Trehalose Glass Is Facilitated by an Emergent Compact Non-Native State. J Phys Chem Lett 2021; 12:7659-7664. [PMID: 34351767 DOI: 10.1021/acs.jpclett.1c02379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
From stem cell freeze-drying to organ storage, considerable recent efforts have been directed toward the development of new preservation technologies. A prominent protein stabilizing strategy involves vitrification in glassy matrices, most notably those formed of sugars such as the biologically relevant preservative trehalose. Here, we compare the folding thermodynamics of a model miniprotein in solution and in the glassy state of the sugars trehalose and glucose. Using synchrotron radiation circular dichroism (SRCD), we find that the same native structure persists in solution and glass. However, upon transition to the glass, a completely different, conformationally restricted unfolded state replaces the disordered denatured state found in solution, potentially inhibiting misfolding. Concomitantly, a large exothermic contribution is observed in glass, exposing the stabilizing effect of interactions with the sugar matrix on the native state. Our results shed light on the mechanism of protein stabilization in sugar glass and should aid in future preservation technologies.
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Affiliation(s)
- Gil I Olgenblum
- Institute of Chemistry, the Fritz Haber Research Center, and the Harvey M. Kruger Center for Nanoscience & Nanotechnology, The Hebrew University, Jerusalem, 9190401, Israel
| | - Frank Wien
- DISCO Beamline, Synchrotron SOLEIL, 91192 Gif-sur-Yvette, France
| | - Liel Sapir
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Daniel Harries
- Institute of Chemistry, the Fritz Haber Research Center, and the Harvey M. Kruger Center for Nanoscience & Nanotechnology, The Hebrew University, Jerusalem, 9190401, Israel
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12
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The kinetics of islet amyloid polypeptide phase-separated system and hydrogel formation are critically influenced by macromolecular crowding. Biochem J 2021; 478:3025-3046. [PMID: 34313292 PMCID: PMC8370757 DOI: 10.1042/bcj20210384] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/19/2021] [Accepted: 07/26/2021] [Indexed: 11/17/2022]
Abstract
Many protein misfolding diseases (e.g. type II diabetes and Alzheimer's disease) are characterised by amyloid deposition. Human islet amyloid polypeptide (hIAPP, involved in type II diabetes) spontaneously undergoes liquid-liquid phase separation (LLPS) and a kinetically complex hydrogelation, both catalysed by hydrophobic-hydrophilic interfaces (e.g. air-water interface and/or phospholipids-water interfaces). Gelation of hIAPP phase-separated liquid droplets initiates amyloid aggregation and the formation of clusters of interconnected aggregates, which grow and fuse to eventually percolate the whole system. Droplet maturation into irreversible hydrogels via amyloid aggregation is thought to be behind the pathology of several diseases. Biological fluids contain a high volume fraction of macromolecules, leading to macromolecular crowding. Despite crowding agent addition in in vitro studies playing a significant role in changing protein phase diagrams, the mechanism underlying enhanced LLPS, and the effect(s) on stages beyond LLPS remain poorly or not characterised.We investigated the effect of macromolecular crowding and increased viscosity on the kinetics of hIAPP hydrogelation using rheology and the evolution of the system beyond LLPS by microscopy. We demonstrate that increased viscosity exacerbated the kinetic variability of hydrogelation and of the phase separated-aggregated system, whereas macromolecular crowding abolished heterogeneity. Increased viscosity also strengthened the gel meshwork and accelerated aggregate cluster fusion. In contrast, crowding either delayed cluster fusion onset (dextran) or promoted it (Ficoll). Our study highlights that an in vivo crowded environment would critically influence amyloid stages beyond LLPS and pathogenesis.
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13
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Garfagnini T, Levi-Kalisman Y, Harries D, Friedler A. Osmolytes and crowders regulate aggregation of the cancer-related L106R mutant of the Axin protein. Biophys J 2021; 120:3455-3469. [PMID: 34087214 DOI: 10.1016/j.bpj.2021.05.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 05/28/2021] [Indexed: 11/16/2022] Open
Abstract
Protein aggregation is involved in a variety of diseases, including neurodegenerative diseases and cancer. The cellular environment is crowded by a plethora of cosolutes comprising small molecules and biomacromolecules at high concentrations, which may influence the aggregation of proteins in vivo. To account for the effect of cosolutes on cancer-related protein aggregation, we studied their effect on the aggregation of the cancer-related L106R mutant of the Axin protein. Axin is a key player in the Wnt signaling pathway, and the L106R mutation in its RGS domain results in a native molten globule that tends to form native-like aggregates. This results in uncontrolled activation of the Wnt signaling pathway, leading to cancer. We monitored the aggregation process of Axin RGS L106R in vitro in the presence of a wide ensemble of cosolutes including polyols, amino acids, betaine, and polyethylene glycol crowders. Except myo-inositol, all polyols decreased RGS L106R aggregation, with carbohydrates exerting the strongest inhibition. Conversely, betaine and polyethylene glycols enhanced aggregation. These results are consistent with the reported effects of osmolytes and crowders on the stability of molten globular proteins and with both amorphous and amyloid aggregation mechanisms. We suggest a model of Axin L106R aggregation in vivo, whereby molecularly small osmolytes keep the protein as a free soluble molecule but the increased crowding of the bound state by macromolecules induces its aggregation at the nanoscale. To our knowledge, this is the first systematic study on the effect of osmolytes and crowders on a process of native-like aggregation involved in pathology, as it sheds light on the contribution of cosolutes to the onset of cancer as a protein misfolding disease and on the relevance of aggregation in the molecular etiology of cancer.
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Affiliation(s)
- Tommaso Garfagnini
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yael Levi-Kalisman
- The Harvey M. Krueger Family Center for Nanoscience and Nanotechnology and The Alexander Silberman Life Sciences Institute, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Daniel Harries
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel; The Fritz Haber Center, The Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Assaf Friedler
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel.
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Response to crowded conditions reveals compact nucleus for amyloid formation of folded protein. QRB DISCOVERY 2021. [PMID: 37529678 PMCID: PMC10392690 DOI: 10.1017/qrd.2020.17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Abstract
Although the consequences of the crowded cell environments may affect protein folding, function and misfolding reactions, these processes are often studied in dilute solutions in vitro. We here used biophysical experiments to investigate the amyloid fibril formation process of the fish protein apo-β-parvalbumin in solvent conditions that mimic steric and solvation aspects of the in vivo milieu. Apo-β-parvalbumin is a folded protein that readily adopts an amyloid state via a nucleation–elongation mechanism. Aggregation experiments in the presence of macromolecular crowding agents (probing excluded volume, entropic effects) as well as small molecule osmolytes (probing solvation, enthalpic effects) revealed that both types of agents accelerate overall amyloid formation, but the elongation step was faster with macromolecular crowding agents but slower in the presence of osmolytes. The observations can be explained by the steric effects of excluded volume favoring assembled states and that amyloid nucleation does not involve monomer unfolding. In contrast, the solvation effects due to osmolyte presence promote nucleation but not elongation. Therefore, the amyloid-competent nuclei must be compact with less osmolytes excluded from the surface than either the folded monomers or amyloid fibers. We conclude that, in contrast to other amyloidogenic folded proteins, amyloid formation of apo-β-parvalbumin is accelerated by crowded cell-like conditions due to a nucleation process that does not involve large-scale protein unfolding.
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15
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Parveen R, Tarannum Z, Ali S, Fatima S. Nanoclay based study on protein stability and aggregation and its implication in human health. Int J Biol Macromol 2020; 166:385-400. [PMID: 33122071 DOI: 10.1016/j.ijbiomac.2020.10.197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/09/2020] [Accepted: 10/24/2020] [Indexed: 10/23/2022]
Abstract
Protein aggregation is the major cause of several acute amyloid diseases such as Parkinson's, Huntington's, Alzheimer's, Lysozyme Systemic amyloidosis, Diabetes-II etc. While these diseases have attracted much attention but the cure is still unavailable. In the present study, Human Serum Albumin (HSA) and Human Lysozyme (HL) were used as the model proteins to investigate their aggregations. Nanoclays are hydrous silicates found in clay fraction of soil and known as natural nanomaterials. They have long been used in several applications in health-related products. In the present paper, the different types of nanoclays (MMT K-10, MMT K-30, Halloysite, Bentonite) were used to inhibit the process of HSA and HL aggregation. Aggregation experiments were evaluated using several biophysical tools such as Turbidity measurements, Intrinsic fluorescence, 1-anilino-8-naphthalene sulfonate (ANS), Thioflavin T (Th T), congo red (CR) binding assays and Circular dichroism. Results demonstrated that all the nanoclays inhibit the DTT-induced aggregation. However, bentonite and MMT K-10 were progressively intense and potent as they slowed down nucleation stage which can be perceived using several biophysical techniques. Hence, nanoclays can be used as an artificial chaperone and might provide effective treatment against several protein aggregation related disorders.
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Affiliation(s)
- Romana Parveen
- Department of Biotechnology, Jamia Millia Islamia, New Delhi 110025, India
| | - Zeba Tarannum
- Department of Biotechnology, Jamia Millia Islamia, New Delhi 110025, India
| | - Sher Ali
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Sadaf Fatima
- Department of Biotechnology, Jamia Millia Islamia, New Delhi 110025, India.
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16
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Stressing crystals with solutes: Effects of added solutes on crystalline caffeine and their relevance to determining transfer free energies. Colloids Surf A Physicochem Eng Asp 2020. [DOI: 10.1016/j.colsurfa.2020.124889] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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17
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Disorder under stress: Role of polyol osmolytes in modulating fibrillation and aggregation of intrinsically disordered proteins. Biophys Chem 2020; 264:106422. [PMID: 32707418 DOI: 10.1016/j.bpc.2020.106422] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/19/2020] [Accepted: 06/20/2020] [Indexed: 12/18/2022]
Abstract
Intrinsically disordered proteins (IDPs) comprise ~30-40% of the proteome, have key roles in cellular processes, and have been reported to be involved in stress regulation working in synergy with osmolytes. Osmolytes are known to accumulate against various stresses in living systems and are known to stabilize the native conformation of globular proteins. However, little is known of their effect on IDPs and their mechanism of action is unclear. We have investigated the effect of a series of polyol osmolytes on the conformation, aggregation and fibrillation properties of the IDPs α and β-synuclein, involved in Parkinson's disease, using fluorescence, CD, light scattering and TEM. We observe inhibition of fibril and aggregate formation with increasing concentration as well as the number of hydroxyl groups in polyols as observed by light scattering measurements which correlates well with the increase in viscosity of solution with increasing number of OH groups in them. However, ThT assay, while indicating suppression of fibril formation at various concentrations of polyols, shows enhanced fibrillation at some other concentrations which could be due to the heterogeneity of the species formed that are ThT insensitive. Fibril formation was, thus, probed by using Nile red fluorescence which showed sensitivity towards the species formed. ANS binding fluorescence also indicates a decrease in the hydrophobicity of the fibrils with increasing number of OH groups in polyols. Polyols do not have any effect on the fibrillation of β-syn but lead to enhanced amorphous aggregate formation in presence of Ethylene Glycol and Glycerol and a reduction in the presence of Sorbitol. The net free energy of transfer of the proteins from water to Sorbitol is large and positive while it is relatively negligible in the case of Glycerol suggestive of greater preferential exclusion effect of Sorbitol in comparison with Glycerol in the case of IDPs as well. The results overall show differential and complex effect of osmolytes towards the fibrillation/aggregation properties of the two IDPs and suggest that an appropriate balance between the concentration and type of polyol or osmolyte would be required for the survival of organisms rich in IDPs under various stress conditions.
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Hämisch B, Pollak R, Ebbinghaus S, Huber K. Self-Assembly of Pseudo-Isocyanine Chloride as a Sensor for Macromolecular Crowding In Vitro and In Vivo. Chemistry 2020; 26:7041-7050. [PMID: 32154954 PMCID: PMC7317963 DOI: 10.1002/chem.202000113] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 02/20/2020] [Indexed: 11/21/2022]
Abstract
Pseudo‐isocyanine chloride (PIC) is a cationic dyestuff that exhibits self‐assembly in aqueous solution, promoted either by increasing the PIC concentration or by decreasing the temperature. PIC‐aggregates exhibit a characteristic and sharp absorption band as well as a fluorescence band at a wavelength of 573 nm making PIC an interesting candidate to analyze the self‐assembly process in various environments. The present work developed PIC‐based, synthetic model systems, suitable to investigate how macromolecular crowding influences self‐assembly processes. Four synthetic additives were used as potential crowders: Triethylene glycol (TEG), polyethylene glycol (PEG), Ficoll 400 as a highly branched polysaccharide, and sucrose corresponding to the monomeric unit of Ficoll. Combined UV/Vis spectroscopy and time‐resolved light scattering revealed a strong impact of crowding based on excluded volume effects only for Ficoll 400. Sucrose had hardly any influence on the self‐assembly of PIC and PEG and TEG impeded the PIC self‐assembly. Development of such a PIC based model system led over to in‐cell experiments. HeLa cells were infiltrated with PIC solutions well below the aggregation threshold in the infiltrating solution. In the cellular environment, PIC was exposed to a significant crowding and immediately started to aggregate. As was demonstrated by fluorescence imaging, the extent of aggregation can be modulated by exposing the cells to salt‐induced osmotic stress. The results suggest future use of such a system as a sensor for the analysis of in vitro and in vivo crowding effects on self‐assembly processes.
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Affiliation(s)
- Benjamin Hämisch
- Physical Chemistry, Paderborn University, 33098, Paderborn, Germany
| | - Roland Pollak
- Physical and Theoretical Chemistry, TU Braunschweig, 38106, Braunschweig, Germany
| | - Simon Ebbinghaus
- Physical and Theoretical Chemistry, TU Braunschweig, 38106, Braunschweig, Germany
| | - Klaus Huber
- Physical Chemistry, Paderborn University, 33098, Paderborn, Germany
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19
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Sapir L, Harries D. Restructuring a Deep Eutectic Solvent by Water: The Nanostructure of Hydrated Choline Chloride/Urea. J Chem Theory Comput 2020; 16:3335-3342. [PMID: 32223260 DOI: 10.1021/acs.jctc.0c00120] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Deep eutectic mixtures are a promising sustainable and diverse class of tunable solvents that hold great promise for various green chemical and technological processes. Many deep eutectic solvents (DES) are hygroscopic and find use in applications with varying extents of hydration, hence urging a profound understanding of changes in the nanostructure of DES with water content. Here, we report on molecular dynamics simulations of the quintessential choline chloride-urea mixture, using a newly parametrized force field with scaled charges to account for physical properties of hydrated DES mixtures. These simulations indicate that water changes the nanostructure of solution even at very low hydration. We present a novel approach that uses convex constrained analysis to dissect radial distribution functions into base components representing different modes of local association. Specifically, DES mixtures can be deconvoluted locally into two dominant competing nanostructures, whose relative prevalence (but not their salient structural features) change with added water over a wide concentration range, from dry up to ∼30 wt % hydration. Water is found to be associated strongly with several DES components but remarkably also forms linear bead-on-string clusters with chloride. At high water content (beyond ∼50 wt % of water), the solution changes into an aqueous electrolyte-like mixture. Finally, the structural evolution of the solution at the nanoscale with extent of hydration is echoed in the DES macroscopic material properties. These changes to structure, in turn, should prove important in the way DES acts as a solvent and to its interactions with additive components.
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Affiliation(s)
- Liel Sapir
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Daniel Harries
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, and The Fritz Haber Research Center, The Hebrew University, Jerusalem 9190401, Israel
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20
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Olgenblum GI, Sapir L, Harries D. Properties of Aqueous Trehalose Mixtures: Glass Transition and Hydrogen Bonding. J Chem Theory Comput 2020; 16:1249-1262. [PMID: 31917927 PMCID: PMC7467637 DOI: 10.1021/acs.jctc.9b01071] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Trehalose is a naturally occurring disaccharide known to remarkably stabilize biomacromolecules in the biologically active state. The stabilizing effect is typically observed over a large concentration range and affects many macromolecules including proteins, lipids, and DNA. Of special interest is the transition from aqueous solution to the dense and highly concentrated glassy state of trehalose that has been implicated in bioadaptation of different organisms toward desiccation stress. Although several mechanisms have been suggested to link the structure of the low water content glass with its action as an exceptional stabilizer, studies are ongoing to resolve which are most pertinent. Specifically, the role that hydrogen bonding plays in the formation of the glass is not well resolved. Here we model aqueous trehalose mixtures over a wide concentration range, using molecular dynamics simulations with two available force fields. Both force fields indicate glass transition temperatures and osmotic pressures that are close to experimental values, particularly at high trehalose contents. We develop and employ a methodology that allows us to analyze the thermodynamics of hydrogen bonds in simulations at different water contents and temperatures. Remarkably, this analysis is able to link the liquid to glass transition with changes in hydrogen bond characteristics. Most notably, the onset of the glassy state can be quantitatively related to the transition from weakly to strongly correlated hydrogen bonds. Our findings should help resolve the properties of the glass and the mechanisms of its formation in the presence of added macromolecules.
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Affiliation(s)
- Gil I Olgenblum
- Institute of Chemistry, the Fritz Haber Research Center, and the Harvey M. Kruger Center for Nanoscience & Nanotechnology , The Hebrew University , Jerusalem 9190401 , Israel
| | - Liel Sapir
- Department of Mechanical Engineering and Materials Science , Duke University , Durham , North Carolina 27708 , United States
| | - Daniel Harries
- Institute of Chemistry, the Fritz Haber Research Center, and the Harvey M. Kruger Center for Nanoscience & Nanotechnology , The Hebrew University , Jerusalem 9190401 , Israel
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21
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Sukenik S, Salam M, Wang Y, Gruebele M. In-Cell Titration of Small Solutes Controls Protein Stability and Aggregation. J Am Chem Soc 2018; 140:10497-10503. [DOI: 10.1021/jacs.8b04809] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Shahar Sukenik
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Mohammed Salam
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Yuhan Wang
- Center for Biophysics and Quantitative Biology, University of Illinois, Urbana, Illinois 61801, United States
| | - Martin Gruebele
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
- Center for Biophysics and Quantitative Biology, University of Illinois, Urbana, Illinois 61801, United States
- Department of Physics, University of Illinois, Urbana, Illinois 61801, United States
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22
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23
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Oyetayo OO, Méndez-Lucio O, Bender A, Kiefer H. Towards understanding polyol additive effects on the pH shift-induced aggregation of a monoclonal antibody using high throughput screening and quantitative structure-activity modeling. Int J Pharm 2017; 530:165-172. [DOI: 10.1016/j.ijpharm.2017.07.059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 07/18/2017] [Accepted: 07/20/2017] [Indexed: 11/16/2022]
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24
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25
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Kong LX, Zeng CM. Effects of Seeding on Lysozyme Amyloid Fibrillation in the Presence of Epigallocatechin and Polyethylene Glycol. BIOCHEMISTRY (MOSCOW) 2017; 82:156-167. [PMID: 28320299 DOI: 10.1134/s0006297917020079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Preformed amyloid fibrils can act as seeds for accelerating protein fibrillation. In the present study, we examined the effects of preformed seeds on lysozyme amyloid fibrillation in the presence of two distinct inhibitors - epigallocatechin (EGC) and polyethylene glycol 2000 (PEG). The results demonstrated that the effects of fibrillar seeds on the acceleration of lysozyme fibrillation depended on the aggregation pathway directed by an inhibitor. EGC inhibited lysozyme fibrillation and modified the peptide chains with quinone moieties in a concentration-dependent manner. The resulting aggregates showed amorphous off-pathway morphology. Preformed fibril seeds did not promote lysozyme fibrillation in the presence of EGC. PEG also inhibited lysozyme fibrillation, and the resulting aggregates showed on-pathway protofibrillar morphology. In contrast, the addition of fibril seeds into the mixture of lysozyme and PEG significantly stimulated fibril growth. Assays of cell viability showed that both EGC and PEG inhibited the formation of cytotoxic species. In accordance with thioflavine T data, the seeds failed to alter the cell-damaging potency of the EGC-directed off-pathway aggregates, but increased the cytotoxicity of the PEG-directed on-pathway fibrils. We suggest that the pattern of interaction between lysozyme and an inhibitor determines the pathway of aggregation and therefore the effects of seeding on amyloid formation. EGC covalently modified lysozyme chains with quinones, directing the aggregation to proceed through an off-pathway, whereas PEG affected the protein in a noncovalent manner, and fibril growth could be stimulated under seeding through an on-pathway.
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Affiliation(s)
- Li-Xiu Kong
- Shaanxi Normal University, School of Chemistry and Chemical Engineering, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Xi'an, 710119, China.
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26
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Shahid S, Hassan MI, Islam A, Ahmad F. Size-dependent studies of macromolecular crowding on the thermodynamic stability, structure and functional activity of proteins: in vitro and in silico approaches. Biochim Biophys Acta Gen Subj 2017; 1861:178-197. [DOI: 10.1016/j.bbagen.2016.11.014] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 11/09/2016] [Accepted: 11/10/2016] [Indexed: 11/27/2022]
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27
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Luo XD, Kong FL, Dang HB, Chen J, Liang Y. Macromolecular crowding favors the fibrillization of β2-microglobulin by accelerating the nucleation step and inhibiting fibril disassembly. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1609-19. [DOI: 10.1016/j.bbapap.2016.07.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 07/23/2016] [Accepted: 07/28/2016] [Indexed: 12/21/2022]
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28
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Khan MV, Ishtikhar M, Rabbani G, Zaman M, Abdelhameed AS, Khan RH. Polyols (Glycerol and Ethylene glycol) mediated amorphous aggregate inhibition and secondary structure restoration of metalloproteinase-conalbumin (ovotransferrin). Int J Biol Macromol 2016; 94:290-300. [PMID: 27744055 PMCID: PMC7112414 DOI: 10.1016/j.ijbiomac.2016.10.023] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 10/10/2016] [Indexed: 11/24/2022]
Abstract
Conalbumin aggregates at 65 °C and denaturation occur at above this temperature. The nature of aggregates was identified as amorphous. The polyols inhibits the aggregation of conalbumin via protecting the secondary structure. Glycerol is found to be more protective than ethylene glycol.
Under physical or chemical stress, proteins tend to form aggregates either highly ordered (amyloid) or unordered (amorphous) causing many pathological disorders in human and loss of proteins functionality in both laboratory conditions and industries during production and storage at commercial level. We investigated the effect of increasing temperature on Conalbumin (CA) and induced aggregation at 65 °C. The enhanced Thioflavin T (ThT) and ANS (1-anilinonaphtalene 8-sulfonic acid) fluorescence intensity, show no shift on Congo red binding, additionally, transmission and scanning electron microscopy (TEM) (SEM) reveal amorphous morphology of the aggregate. Our investigation clearly demonstrated that polyols namely Glycerol (GL) and Ethylene glycol (EG) are so staunch to inhibit amorphous aggregates via restoring secondary conformation. Addition of polyols (15% GL and 35% EG) significantly decrease the turbidity, Rayleigh scattering ThT and ANS fluorescence intensity. The dynamic light scattering (DLS) data show that hydrodynamic radii (Rh) of the aggregates is ∼20 times higher than native CA while nearly similar for GL and EG protected CA due to condensation of core size with little difference.
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Affiliation(s)
- Mohsin Vahid Khan
- Molecular Biophysics and Biophysical Chemistry Group, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India
| | - Mohd Ishtikhar
- Molecular Biophysics and Biophysical Chemistry Group, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India
| | - Gulam Rabbani
- Molecular Biophysics and Biophysical Chemistry Group, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India
| | - Masihuz Zaman
- Molecular Biophysics and Biophysical Chemistry Group, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India
| | - Ali Saber Abdelhameed
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Rizwan Hasan Khan
- Molecular Biophysics and Biophysical Chemistry Group, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India.
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Effects of hydrophobic macromolecular crowders on amyloid β (16-22) aggregation. Biophys J 2016; 109:124-34. [PMID: 26153709 DOI: 10.1016/j.bpj.2015.05.032] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 05/15/2015] [Accepted: 05/28/2015] [Indexed: 11/24/2022] Open
Abstract
In Alzheimer's disease (AD), the amyloid β (Aβ) peptide aggregates in the brain to form progressively larger oligomers, fibrils, and plaques. The aggregation process is strongly influenced by the presence of other macromolecular species, called crowders, that can exert forces on the proteins. One very common attribute of macromolecular crowders is their hydrophobicity. We examined the effect of hydrophobic crowders on protein aggregation by using discontinuous molecular dynamics (DMD) simulations in combination with an intermediate resolution protein model, PRIME20. The systems considered contained 48 Aβ (16-22) peptides and crowders with diameters of 5 Å, 20 Å, and 40 Å, represented by hard spheres or spheres with square-well/square-shoulder interactions, at a crowder volume fraction of ϕ = 0.10. Results show that low levels of crowder hydrophobicity are capable of increasing the fibrillation lag time and high levels of crowder hydrophobicity can fully prevent the formation of fibrils. The types of structures that remain during the final stages of the simulations are summarized in a global phase diagram that shows fibril, disordered oligomer, or β-sheet phases in the space spanned by crowder size and crowder hydrophobicity. In particular, at high levels of hydrophobicity, simulations with 5 Å crowders result in only disordered oligomers and simulations with 40 Å crowders result in only β-sheets. The presence of hydrophobic crowders reduces the antiparallel β-sheet content of fibrils, whereas hard sphere crowders increase it. Finally, strong hydrophobic crowders alter the secondary structure of the Aβ (16-22) monomers, bending them into a shape that is incapable of forming ordered β-sheets or fibrils. These results qualitatively agree with previous theoretical and experimental work.
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Chaturvedi SK, Khan JM, Siddiqi MK, Alam P, Khan RH. Comparative insight into surfactants mediated amyloidogenesis of lysozyme. Int J Biol Macromol 2016; 83:315-25. [DOI: 10.1016/j.ijbiomac.2015.11.053] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 11/18/2015] [Accepted: 11/19/2015] [Indexed: 12/14/2022]
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31
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Ishtikhar M, Ali MS, Atta AM, Al-Lohedan H, Badr G, Khan RH. Temperature dependent rapid annealing effect induces amorphous aggregation of human serum albumin. Int J Biol Macromol 2016; 82:844-55. [DOI: 10.1016/j.ijbiomac.2015.10.071] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 10/21/2015] [Indexed: 10/22/2022]
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32
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Sukenik S, Sapir L, Harries D. Osmolyte Induced Changes in Peptide Conformational Ensemble Correlate with Slower Amyloid Aggregation: A Coarse-Grained Simulation Study. J Chem Theory Comput 2015; 11:5918-28. [DOI: 10.1021/acs.jctc.5b00657] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shahar Sukenik
- Institute of Chemistry and
the Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
| | - Liel Sapir
- Institute of Chemistry and
the Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
| | - Daniel Harries
- Institute of Chemistry and
the Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
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33
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Breydo L, Sales AE, Frege T, Howell MC, Zaslavsky BY, Uversky VN. Effects of Polymer Hydrophobicity on Protein Structure and Aggregation Kinetics in Crowded Milieu. Biochemistry 2015; 54:2957-66. [PMID: 25919930 DOI: 10.1021/acs.biochem.5b00116] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We examined the effects of water-soluble polymers of various degrees of hydrophobicity on the folding and aggregation of proteins. The polymers we chose were polyethylene glycol (PEG) and UCON (1:1 copolymer of ethylene glycol and propylene glycol). The presence of additional methyl groups in UCON makes it more hydrophobic than PEG. Our earlier analysis revealed that similarly sized PEG and UCON produced different changes in the solvent properties of water in their solutions and induced morphologically different α-synuclein aggregates [Ferreira, L. A., et al. (2015) Role of solvent properties of aqueous media in macromolecular crowding effects. J. Biomol. Struct. Dyn., in press]. To improve our understanding of molecular mechanisms defining behavior of proteins in a crowded environment, we tested the effects of these polymers on secondary and tertiary structure and aromatic residue solvent accessibility of 10 proteins [five folded proteins, two hybrid proteins; i.e., protein containing ordered and disordered domains, and three intrinsically disordered proteins (IDPs)] and on the aggregation kinetics of insulin and α-synuclein. We found that effects of both polymers on secondary and tertiary structures of folded and hybrid proteins were rather limited with slight unfolding observed in some cases. Solvent accessibility of aromatic residues was significantly increased for the majority of the studied proteins in the presence of UCON but not PEG. PEG also accelerated the aggregation of protein into amyloid fibrils, whereas UCON promoted aggregation to amyloid oligomers instead. These results indicate that even a relatively small change in polymer structure leads to a significant change in the effect of this polymer on protein folding and aggregation. This is an indication that protein folding and especially aggregation are highly sensitive to the presence of other macromolecules, and an excluded volume effect is insufficient to describe their effect.
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34
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Ishtikhar M, Usmani SS, Gull N, Badr G, Mahmoud MH, Khan RH. Inhibitory effect of copper nanoparticles on rosin modified surfactant induced aggregation of lysozyme. Int J Biol Macromol 2015; 78:379-88. [DOI: 10.1016/j.ijbiomac.2015.03.069] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2014] [Revised: 03/10/2015] [Accepted: 03/12/2015] [Indexed: 12/19/2022]
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35
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Murray B, Rosenthal J, Zheng Z, Isaacson D, Zhu Y, Belfort G. Cosolute effects on amyloid aggregation in a nondiffusion limited regime: intrinsic osmolyte properties and the volume exclusion principle. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:4246-4254. [PMID: 25803421 DOI: 10.1021/acs.langmuir.5b00254] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The effects of cosolutes on amyloid aggregation kinetics in vivo are critical and not fully understood. To explore the effects of cosolute additives, the in vitro behavior of destabilizing and stabilizing osmolytes with polymer cosolutes on the aggregation of a model amyloid, human insulin, is probed using experiments coupled with an amyloid aggregation reaction model. The destabilizing osmolyte, guanidine hydrochloride (GuHCl), induces biphasic behavior on the amyloid aggregation rate exhibited by an enhancement of the aggregation kinetics at low concentrations of GuHCl (<0.6 M) and a reduction in kinetics at higher GuHCl concentrations. Stabilizing osmolytes, glycerol, sorbitol and trimethylamine N-oxide, slow the rate of aggregation by reducing the rate of monomer unfolding. Polymer cosolutes, polyvinylpyrrolidone 3.5 kDa and 40 kDa, delay amyloid aggregation mainly through a decrease in the nucleation reaction. These results are in good agreement with the volume exclusion principle for polymer crowding and supports the need to include conformational rearrangement of monomers prior to nucleation. Using fluorescence correlation spectroscopy, we demonstrate that amyloid aggregation is nondiffusion limited, except during fibril accumulation in the presence of high concentrations of long chain polymers. Lastly, the neutral surface area of osmolytes correlates well with the time to initiate fibril formation, tlag, which implicates an intrinsic osmolyte property underlying preferential interactions.
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Affiliation(s)
| | | | - Zhongli Zheng
- §Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | | | - Yingxi Zhu
- §Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
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36
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Thermodynamics and solvent linkage of macromolecule-ligand interactions. Methods 2014; 76:51-60. [PMID: 25462561 DOI: 10.1016/j.ymeth.2014.11.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 11/11/2014] [Accepted: 11/13/2014] [Indexed: 02/06/2023] Open
Abstract
Binding involves two steps, desolvation and association. While water is ubiquitous and occurs at high concentration, it is typically ignored. In vitro experiments typically use infinite dilution conditions, while in vivo, the concentration of water is decreased due to the presence of high concentrations of molecules in the cellular milieu. This review discusses isothermal titration calorimetry approaches that address the role of water in binding. For example, use of D2O allows the contribution of solvent reorganization to the enthalpy component to be assessed. Further, the addition of osmolytes will decrease the water activity of a solution and allow effects on Ka to be determined. In most cases, binding becomes tighter in the presence of osmolytes as the desolvation penalty associated with binding is minimized. In other cases, the osmolytes prefer to interact with the ligand or protein, and if their removal is more difficult than shedding water, then binding can be weakened. These complicating layers can be discerned by different slopes in ln(Ka) vs osmolality plots and by differential scanning calorimetry in the presence of the osmolyte.
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37
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Latshaw DC, Cheon M, Hall CK. Effects of macromolecular crowding on amyloid beta (16-22) aggregation using coarse-grained simulations. J Phys Chem B 2014; 118:13513-26. [PMID: 25347801 PMCID: PMC4254002 DOI: 10.1021/jp508970q] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
![]()
To
examine the effect of crowding on protein aggregation, discontinuous
molecular dynamics (DMD) simulations combined with an intermediate
resolution protein model, PRIME20, were applied to a peptide/crowder
system. The systems contained 192 Aβ(16–22) peptides
and crowders of diameters 5, 20, and 40 Å, represented here by
simple hard spheres, at crowder volume fractions of 0.00, 0.10, and
0.20. Results show that both crowder volume fraction and crowder diameter
have a large impact on fibril and oligomer formation. The addition
of crowders to a system of peptides increases the rate of oligomer
formation, shifting from a slow ordered formation of oligomers in
the absence of crowders, similar to nucleated polymerization, to a
fast collapse of peptides and subsequent rearrangement characteristic
of nucleated conformational conversion with a high maximum in the
number of peptides in oligomers as the total crowder surface area
increases. The rate of conversion from oligomers to fibrils also increases
with increasing total crowder surface area, giving rise to an increased
rate of fibril growth. In all cases, larger volume fractions and smaller
crowders provide the greatest aggregation enhancement effects. We
also show that the size of the crowders influences the formation of
specific oligomer sizes. In our simulations, the 40 Å crowders
enhance the number of dimers relative to the numbers of trimers, hexamers,
pentamers, and hexamers, while the 5 Å crowders enhance the number
of hexamers relative to the numbers of dimers, trimers, tetramers,
and pentamers. These results are in qualitative agreement with previous
experimental and theoretical work.
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Affiliation(s)
- David C Latshaw
- Center for Proteome Biophysics, Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST) , Daegu 711-873, Korea
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38
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Crowded milieu prevents fibrillation of hen egg white lysozyme with retention of enzymatic activity. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2014; 138:8-16. [DOI: 10.1016/j.jphotobiol.2014.04.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 04/22/2014] [Accepted: 04/24/2014] [Indexed: 11/18/2022]
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39
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Theillet FX, Binolfi A, Frembgen-Kesner T, Hingorani K, Sarkar M, Kyne C, Li C, Crowley PB, Gierasch L, Pielak GJ, Elcock AH, Gershenson A, Selenko P. Physicochemical properties of cells and their effects on intrinsically disordered proteins (IDPs). Chem Rev 2014; 114:6661-714. [PMID: 24901537 PMCID: PMC4095937 DOI: 10.1021/cr400695p] [Citation(s) in RCA: 338] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Indexed: 02/07/2023]
Affiliation(s)
- Francois-Xavier Theillet
- Department
of NMR-supported Structural Biology, In-cell NMR Laboratory, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Robert-Roessle Strasse 10, 13125 Berlin, Germany
| | - Andres Binolfi
- Department
of NMR-supported Structural Biology, In-cell NMR Laboratory, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Robert-Roessle Strasse 10, 13125 Berlin, Germany
| | - Tamara Frembgen-Kesner
- Department
of Biochemistry, University of Iowa, Bowen Science Building, 51 Newton
Road, Iowa City, Iowa 52242, United States
| | - Karan Hingorani
- Departments
of Biochemistry & Molecular Biology and Chemistry, Program in
Molecular & Cellular Biology, University
of Massachusetts, Amherst, 240 Thatcher Way, Amherst, Massachusetts 01003, United States
| | - Mohona Sarkar
- Department
of Chemistry, Department of Biochemistry and Biophysics and Lineberger
Comprehensive Cancer Center, University
of North Carolina, Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Ciara Kyne
- School
of Chemistry, National University of Ireland,
Galway, University Road, Galway, Ireland
| | - Conggang Li
- Key Laboratory
of Magnetic Resonance in Biological Systems, State Key Laboratory
of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Center
for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, P.R. China
| | - Peter B. Crowley
- School
of Chemistry, National University of Ireland,
Galway, University Road, Galway, Ireland
| | - Lila Gierasch
- Departments
of Biochemistry & Molecular Biology and Chemistry, Program in
Molecular & Cellular Biology, University
of Massachusetts, Amherst, 240 Thatcher Way, Amherst, Massachusetts 01003, United States
| | - Gary J. Pielak
- Department
of Chemistry, Department of Biochemistry and Biophysics and Lineberger
Comprehensive Cancer Center, University
of North Carolina, Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Adrian H. Elcock
- Department
of Biochemistry, University of Iowa, Bowen Science Building, 51 Newton
Road, Iowa City, Iowa 52242, United States
| | - Anne Gershenson
- Departments
of Biochemistry & Molecular Biology and Chemistry, Program in
Molecular & Cellular Biology, University
of Massachusetts, Amherst, 240 Thatcher Way, Amherst, Massachusetts 01003, United States
| | - Philipp Selenko
- Department
of NMR-supported Structural Biology, In-cell NMR Laboratory, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Robert-Roessle Strasse 10, 13125 Berlin, Germany
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40
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Khan JM, Chaturvedi SK, Rahman SK, Ishtikhar M, Qadeer A, Ahmad E, Khan RH. Protonation favors aggregation of lysozyme with SDS. SOFT MATTER 2014; 10:2591-2599. [PMID: 24647567 DOI: 10.1039/c3sm52435c] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Different proteins have different amino acid sequences as well as conformations, and therefore different propensities to aggregate. Electrostatic interactions have an important role in the aggregation of proteins as revealed by our previous report (J. M. Khan et al., PLoS One, 2012, 7, e29694). In this study, we designed and executed experiments to gain knowledge of the role of charge variations on proteins during the events of protein aggregation with lysozyme as a model protein. To impart positive and negative charges to proteins, we incubated lysozyme at different pH values of below and above the pI (∼11). Negatively charged SDS was used to 'antagonize' positive charges on lysozyme. We examined the effects of pH variations on SDS-induced amyloid fibril formation by lysozyme using methods such as far-UV circular dichroism, Rayleigh scattering, turbidity measurements, dye binding assays and dynamic light scattering. We found that sub-micellar concentrations of SDS (0.1 to 0.6 mM) induced amyloid fibril formation by lysozyme in the pH range of 10.0-1.0 and maximum aggregation was observed at pH 1.0. The morphology of aggregates was fibrillar in structure, as visualized by transmission electron microscopy. Isothermal titration calorimetry studies demonstrated that fibril formation is exothermic. To the best of our current understanding of the mechanism of aggregation, this study demonstrates the crucial role of electrostatic interactions during amyloid fibril formation. The model proposed here will help in designing molecules that can prevent or reverse the amyloid fibril formation or the aggregation.
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Affiliation(s)
- Javed M Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India.
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41
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Abstract
Solutes excluded from macromolecules or colloids are known to drive depletion attractions. The established Asakura-Oosawa model, as well as subsequent theories aimed at explaining the effects of macromolecular crowding, attribute depletion forces to diminished hard-core excluded volume upon compaction, and hence predict depletion forces dominated by entropy. However, recent experiments measuring the effect of preferentially excluded solutes on protein folding and macromolecular association find these forces can also be enthalpic. We use simulations of macromolecular association in explicit binary cosolute-solvent mixtures, with solvent and cosolute intermolecular interactions that go beyond hard-cores, to show that not all cosolutes conform to the established entropically dominated model. We further demonstrate how the enthalpically dominated depletion forces that we find can be well described within an Asakura-Oosawa like model provided that the hard-core macromolecule-cosolute potential of mean force is augmented by a "soft" step-like repulsion.
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Affiliation(s)
- Liel Sapir
- Institute of Chemistry and The Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
| | - Daniel Harries
- Institute of Chemistry and The Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
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42
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The crowd you're in with: Effects of different types of crowding agents on protein aggregation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:346-57. [DOI: 10.1016/j.bbapap.2013.11.004] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2013] [Revised: 11/01/2013] [Accepted: 11/11/2013] [Indexed: 11/21/2022]
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43
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Dave AC, Loveday SM, Anema SG, Jameson GB, Singh H. Modulating β-Lactoglobulin Nanofibril Self-Assembly at pH 2 Using Glycerol and Sorbitol. Biomacromolecules 2013; 15:95-103. [DOI: 10.1021/bm401315s] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Anant C. Dave
- Riddet
Institute, Massey University, Private Bag 11 222, Palmerston North, New Zealand
| | - Simon M. Loveday
- Riddet
Institute, Massey University, Private Bag 11 222, Palmerston North, New Zealand
| | - Skelte G. Anema
- Riddet
Institute, Massey University, Private Bag 11 222, Palmerston North, New Zealand
- Fonterra
Research and Development Centre, Private Bag 11 029, Palmerston North, New Zealand
| | - Geoffrey B. Jameson
- Riddet
Institute, Massey University, Private Bag 11 222, Palmerston North, New Zealand
- Institute
of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North, New Zealand
| | - Harjinder Singh
- Riddet
Institute, Massey University, Private Bag 11 222, Palmerston North, New Zealand
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44
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Sukenik S, Sapir L, Harries D. Balance of enthalpy and entropy in depletion forces. Curr Opin Colloid Interface Sci 2013. [DOI: 10.1016/j.cocis.2013.10.002] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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45
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Ma Q, Hu JY, Chen J, Liang Y. The role of crowded physiological environments in prion and prion-like protein aggregation. Int J Mol Sci 2013; 14:21339-52. [PMID: 24284393 PMCID: PMC3856008 DOI: 10.3390/ijms141121339] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Revised: 09/24/2013] [Accepted: 09/27/2013] [Indexed: 01/07/2023] Open
Abstract
Prion diseases and prion- like protein misfolding diseases are related to the accumulation of abnormal aggregates of the normal host proteins including prion proteins and Tau protein. These proteins possess self-templating and transmissible characteristics. The crowded physiological environments where the aggregation of these amyloidogenic proteins takes place can be imitated in vitro by the addition of macromolecular crowding agents such as inert polysaccharides. In this review, we summarize the aggregation of prion proteins in crowded physiological environments and discuss the role of macromolecular crowding in prion protein aggregation. We also summarize the aggregation of prion- like proteins including human Tau protein, human α-synuclein, and human copper, zinc superoxide dismutase under macromolecular crowding environments and discuss the role of macromolecular crowding in prion- like protein aggregation. The excluded-volume effects caused by macromolecular crowding could accelerate the aggregation of neurodegenerative disease-associated proteins while inhibiting the aggregation of the proteins that are not neurodegenerative disease-associated.
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Affiliation(s)
- Qian Ma
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China.
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46
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Seeliger J, Werkmüller A, Winter R. Macromolecular crowding as a suppressor of human IAPP fibril formation and cytotoxicity. PLoS One 2013; 8:e69652. [PMID: 23922768 PMCID: PMC3726762 DOI: 10.1371/journal.pone.0069652] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Accepted: 06/13/2013] [Indexed: 01/21/2023] Open
Abstract
The biological cell is known to exhibit a highly crowded milieu, which significantly influences protein aggregation and association processes. As several cell degenerative diseases are related to the self-association and fibrillation of amyloidogenic peptides, understanding of the impact of macromolecular crowding on these processes is of high biomedical importance. It is further of particular relevance as most in vitro studies on amyloid aggregation have been performed in diluted solution which does not reflect the complexity of their cellular surrounding. The study presented here focuses on the self-association of the type-2 diabetes mellitus related human islet amyloid polypeptide (hIAPP) in various crowded environments including network-forming macromolecular crowding reagents and protein crowders. It was possible to identify two competing processes: a crowder concentration and type dependent stabilization of globular off-pathway species and a--consequently--retarded or even inhibited hIAPP fibrillation reaction. The cause of these crowding effects was revealed to be mainly excluded volume in the polymeric crowders, whereas non-specific interactions seem to be most dominant in protein crowded environments. Specific hIAPP cytotoxicity assays on pancreatic β-cells reveal non-toxicity for the stabilized globular species, in contrast to the high cytotoxicity imposed by the normal fibrillation pathway. From these findings it can be concluded that cellular crowding is able to effectively stabilize the monomeric conformation of hIAPP, hence enabling the conduction of its normal physiological function and prevent this highly amyloidogenic peptide from cytotoxic aggregation and fibrillation.
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Affiliation(s)
- Janine Seeliger
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry, Technische Universität Dortmund, Dortmund, Germany
| | - Alexander Werkmüller
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry, Technische Universität Dortmund, Dortmund, Germany
| | - Roland Winter
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry, Technische Universität Dortmund, Dortmund, Germany
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47
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Larini L, Shea JE. Double Resolution Model for Studying TMAO/Water Effective Interactions. J Phys Chem B 2013; 117:13268-77. [DOI: 10.1021/jp403635g] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Luca Larini
- Department of Chemistry
and Biochemistry
and of Physics, University of California, Santa Barbara, Santa Barbara, California 93106, United
States
| | - Joan-Emma Shea
- Department of Chemistry
and Biochemistry
and of Physics, University of California, Santa Barbara, Santa Barbara, California 93106, United
States
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48
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Sukenik S, Sapir L, Gilman-Politi R, Harries D. Diversity in the mechanisms of cosolute action on biomolecular processes. Faraday Discuss 2013; 160:225-37; discussion 311-27. [PMID: 23795502 DOI: 10.1039/c2fd20101a] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Numerous cellular cosolutes significantly impact the way that proteins and other biomacromolecules act and interact. We have followed the thermodynamic effect of several cosolute classes, including polymers, cellular osmolytes, and inorganic salts, on the stability of biomolecular folding and complexation. By comparing changes in free energy, enthalpy, and entropy upon cosolutes addition for these processes, we identify several thermodynamically distinct mechanisms. Surprisingly, even while many cosolutes display similar scaling of the change in stabilizing free energy with their concentration, a breakdown of this free energy into enthalpic and entropic contributions distinguishes different families of cosolutes. We discuss how these "thermodynamic fingerprints" can direct towards possible underlying mechanisms that govern the cosolute effect.
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Affiliation(s)
- Shahar Sukenik
- Institute of Chemistry and The Fritz Haber Research Center, The Hebrew University, Jerusalem, Israel
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49
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Vagenende V, Han AX, Pek HB, Loo BLW. Quantifying the molecular origins of opposite solvent effects on protein-protein interactions. PLoS Comput Biol 2013; 9:e1003072. [PMID: 23696727 PMCID: PMC3656110 DOI: 10.1371/journal.pcbi.1003072] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 04/11/2013] [Indexed: 12/21/2022] Open
Abstract
Although the nature of solvent-protein interactions is generally weak and non-specific, addition of cosolvents such as denaturants and osmolytes strengthens protein-protein interactions for some proteins, whereas it weakens protein-protein interactions for others. This is exemplified by the puzzling observation that addition of glycerol oppositely affects the association constants of two antibodies, D1.3 and D44.1, with lysozyme. To resolve this conundrum, we develop a methodology based on the thermodynamic principles of preferential interaction theory and the quantitative characterization of local protein solvation from molecular dynamics simulations. We find that changes of preferential solvent interactions at the protein-protein interface quantitatively account for the opposite effects of glycerol on the antibody-antigen association constants. Detailed characterization of local protein solvation in the free and associated protein states reveals how opposite solvent effects on protein-protein interactions depend on the extent of dewetting of the protein-protein contact region and on structural changes that alter cooperative solvent-protein interactions at the periphery of the protein-protein interface. These results demonstrate the direct relationship between macroscopic solvent effects on protein-protein interactions and atom-scale solvent-protein interactions, and establish a general methodology for predicting and understanding solvent effects on protein-protein interactions in diverse biological environments.
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Affiliation(s)
- Vincent Vagenende
- Bioprocessing Technology Institute, ASTAR (Agency for Science, Technology and Research), Singapore.
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50
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Lampel A, Bram Y, Levy-Sakin M, Bacharach E, Gazit E. The effect of chemical chaperones on the assembly and stability of HIV-1 capsid protein. PLoS One 2013; 8:e60867. [PMID: 23577173 PMCID: PMC3618117 DOI: 10.1371/journal.pone.0060867] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2012] [Accepted: 03/04/2013] [Indexed: 11/18/2022] Open
Abstract
Chemical chaperones are small organic molecules which accumulate in a broad range of organisms in various tissues under different stress conditions and assist in the maintenance of a correct proteostasis under denaturating environments. The effect of chemical chaperones on protein folding and aggregation has been extensively studied and is generally considered to be mediated through non-specific interactions. However, the precise mechanism of action remains elusive. Protein self-assembly is a key event in both native and pathological states, ranging from microtubules and actin filaments formation to toxic amyloids appearance in degenerative disorders, such as Alzheimer's and Parkinson's diseases. Another pathological event, in which protein assembly cascade is a fundamental process, is the formation of virus particles. In the late stage of the virus life cycle, capsid proteins self-assemble into highly-ordered cores, which encapsulate the viral genome, consequently protect genome integrity and mediate infectivity. In this study, we examined the effect of different groups of chemical chaperones on viral capsid assembly in vitro, focusing on HIV-1 capsid protein as a system model. We found that while polyols and sugars markedly inhibited capsid assembly, methylamines dramatically enhanced the assembly rate. Moreover, chemical chaperones that inhibited capsid core formation, also stabilized capsid structure under thermal denaturation. Correspondingly, trimethylamine N-oxide, which facilitated formation of high-order assemblies, clearly destabilized capsid structure under similar conditions. In contrast to the prevailing hypothesis suggesting that chemical chaperones affect proteins through preferential exclusion, the observed dual effects imply that different chaperones modify capsid assembly and stability through different mechanisms. Furthermore, our results indicate a correlation between the folding state of capsid to its tendency to assemble into highly-ordered structures.
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Affiliation(s)
- Ayala Lampel
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Yaron Bram
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Michal Levy-Sakin
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Eran Bacharach
- Department of Cell Research and Immunology, Tel Aviv University, Tel Aviv, Israel
- * E-mail: (EB); (EG)
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
- * E-mail: (EB); (EG)
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