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Woulfe J, Munoz DG, Gray DA, Jinnah HA, Ivanova A. Inosine monophosphate dehydrogenase intranuclear inclusions are markers of aging and neuronal stress in the human substantia nigra. Neurobiol Aging 2024; 134:43-56. [PMID: 37992544 DOI: 10.1016/j.neurobiolaging.2023.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/03/2023] [Accepted: 11/06/2023] [Indexed: 11/24/2023]
Abstract
We explored mechanisms involved in the age-dependent degeneration of human substantia nigra (SN) dopamine (DA) neurons. Owing to its important metabolic functions in post-mitotic neurons, we investigated the developmental and age-associated changes in the purine biosynthetic enzyme inosine monophosphate dehydrogenase (IMPDH). Tissue microarrays prepared from post-mortem samples of SN from 85 neurologically intact participants humans spanning the age spectrum were immunostained for IMPDH combined with other proteins. SN DA neurons contained two types of IMPDH structures: cytoplasmic IMPDH filaments and intranuclear IMPDH inclusions. The former were not age-restricted and may represent functional units involved in sustaining purine nucleotide supply in these highly metabolically active cells. The latter showed age-associated changes, including crystallization, features reminiscent of pathological inclusion bodies, and spatial associations with Marinesco bodies; structures previously associated with SN neuron dysfunction and death. We postulate dichotomous roles for these two subcellularly distinct IMPDH structures and propose a nucleus-based model for a novel mechanism of SN senescence that is independent of previously known neurodegeneration-associated proteins.
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Affiliation(s)
- John Woulfe
- Neuroscience Program, The Ottawa Hospital Research Institute, Ottawa, Ontario, Canada; Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, Ontario, Canada.
| | - David G Munoz
- Li Ka Shing Knowledge Institute & Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada; Department of Laboratory Medicine, St. Michael's Hospital, Unity Health, University of Toronto, Toronto, Ontario, Canada
| | - Douglas A Gray
- Center for Cancer Therapeutics, The Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Hyder A Jinnah
- Departments of Neurology, Human Genetics & Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Alyona Ivanova
- The Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children and Neurosurgery Research Department, St. Michael's Hospital, Toronto Unity Health, Toronto, Ontario, Canada
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2
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Romero-Romero ML, Garcia-Seisdedos H. Agglomeration: when folded proteins clump together. Biophys Rev 2023; 15:1987-2003. [PMID: 38192350 PMCID: PMC10771401 DOI: 10.1007/s12551-023-01172-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 11/25/2023] [Indexed: 01/10/2024] Open
Abstract
Protein self-association is a widespread phenomenon that results in the formation of multimeric protein structures with critical roles in cellular processes. Protein self-association can lead to finite protein complexes or open-ended, and potentially, infinite structures. This review explores the concept of protein agglomeration, a process that results from the infinite self-assembly of folded proteins. We highlight its differences from other better-described processes with similar macroscopic features, such as aggregation and liquid-liquid phase separation. We review the sequence, structural, and biophysical factors influencing protein agglomeration. Lastly, we briefly discuss the implications of agglomeration in evolution, disease, and aging. Overall, this review highlights the need to study protein agglomeration for a better understanding of cellular processes.
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Affiliation(s)
- M. L. Romero-Romero
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology, Dresden, Germany
| | - H. Garcia-Seisdedos
- Department of Structural and Molecular Biology, Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Barcelona, Spain
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Hentschel L, Hansen J, Egelhaaf SU, Platten F. The crystallization enthalpy and entropy of protein solutions: microcalorimetry, van't Hoff determination and linearized Poisson–Boltzmann model of tetragonal lysozyme crystals. Phys Chem Chem Phys 2021; 23:2686-2696. [DOI: 10.1039/d0cp06113a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Microcalorimetric and van't Hoff determinations as well as a theoretical description provide a consistent picture of the crystallization enthalpy and entropy of protein solutions and their dependence on physicochemical solution parameters.
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Affiliation(s)
- Lorena Hentschel
- Condensed Matter Physics Laboratory
- Heinrich Heine University
- 40225 Düsseldorf
- Germany
| | - Jan Hansen
- Condensed Matter Physics Laboratory
- Heinrich Heine University
- 40225 Düsseldorf
- Germany
| | - Stefan U. Egelhaaf
- Condensed Matter Physics Laboratory
- Heinrich Heine University
- 40225 Düsseldorf
- Germany
| | - Florian Platten
- Condensed Matter Physics Laboratory
- Heinrich Heine University
- 40225 Düsseldorf
- Germany
- Institute of Biological Information Processing (IBI-4: Biomacromolecular Systems and Processes)
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5
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Wu K, Gore A, Graham R, Meller R. Solubilization of Cyclosporine in Topical Ophthalmic Formulations: Preformulation Risk Assessment on a New Solid Form. J Pharm Sci 2019; 108:3233-3239. [PMID: 31228492 DOI: 10.1016/j.xphs.2019.06.008] [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: 01/15/2019] [Revised: 05/02/2019] [Accepted: 06/07/2019] [Indexed: 11/19/2022]
Abstract
Owing to the discovery of a less soluble crystalline form (form 2) of cyclosporine (CsA), risks in solubility and physical stability of these formulations need to be revisited. This work focused on understanding the solubility behavior of various CsA forms in different media, including water, castor oil, and selected cosolvent micellar systems. In water, form 2 was approximately 8-9 times less soluble than form 1 (aka. tetragonal dihydrate). In neat nonaqueous solvent, for example, castor oil, form 3 (aka. orthorhombic hydrate) was found to have the lowest solubility and therefore the most stable form. In addition, the solubility-temperature relationship of CsA is complex and solvent-dependent. In aqueous vehicles, retrograde temperature dependence of solubility was observed in aqueous vehicles, that is, the solubility of CsA decreased with temperature, which was attributed to the effect of temperature on the strength of hydrogen bonding interactions; conversely, the solubility of CsA increased with temperature in nonaqueous solvents. In addition, the solubility of these CsA forms was very sensitive to temperature. Temperature-dependent form transformation was also observed in the media studied, with faster form conversion occurring at elevated temperatures. These studies provided key information to support the risk assessment for topical ophthalmic formulation development of CsA.
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Affiliation(s)
- Ke Wu
- Pharmaceutical Development Department, Allergan Plc, Irvine, California 92612.
| | - Anu Gore
- Pharmaceutical Development Department, Allergan Plc, Irvine, California 92612
| | - Richard Graham
- Pharmaceutical Development Department, Allergan Plc, Irvine, California 92612
| | - Richard Meller
- Pharmaceutical Development Department, Allergan Plc, Irvine, California 92612
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6
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Garcia‐Seisdedos H, Villegas JA, Levy ED. Infinite Ansammlungen gefalteter Proteine im Kontext von Evolution, Krankheiten und Proteinentwicklung. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201806092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - José A. Villegas
- Department of Structural BiologyWeizmann Institute of Science Rehovot 7610001 Israel
| | - Emmanuel D. Levy
- Department of Structural BiologyWeizmann Institute of Science Rehovot 7610001 Israel
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7
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Garcia‐Seisdedos H, Villegas JA, Levy ED. Infinite Assembly of Folded Proteins in Evolution, Disease, and Engineering. Angew Chem Int Ed Engl 2019; 58:5514-5531. [PMID: 30133878 PMCID: PMC6471489 DOI: 10.1002/anie.201806092] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 08/06/2018] [Indexed: 12/14/2022]
Abstract
Mutations and changes in a protein's environment are well known for their potential to induce misfolding and aggregation, including amyloid formation. Alternatively, such perturbations can trigger new interactions that lead to the polymerization of folded proteins. In contrast to aggregation, this process does not require misfolding and, to highlight this difference, we refer to it as agglomeration. This term encompasses the amorphous assembly of folded proteins as well as the polymerization in one, two, or three dimensions. We stress the remarkable potential of symmetric homo-oligomers to agglomerate even by single surface point mutations, and we review the double-edged nature of this potential: how aberrant assemblies resulting from agglomeration can lead to disease, but also how agglomeration can serve in cellular adaptation and be exploited for the rational design of novel biomaterials.
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Affiliation(s)
| | - José A. Villegas
- Department of Structural BiologyWeizmann Institute of ScienceRehovot7610001Israel
| | - Emmanuel D. Levy
- Department of Structural BiologyWeizmann Institute of ScienceRehovot7610001Israel
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8
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Schönherr R, Rudolph JM, Redecke L. Protein crystallization in living cells. Biol Chem 2019; 399:751-772. [PMID: 29894295 DOI: 10.1515/hsz-2018-0158] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 05/07/2018] [Indexed: 11/15/2022]
Abstract
Protein crystallization in living cells has been observed surprisingly often as a native assembly process during the past decades, and emerging evidence indicates that this phenomenon is also accessible for recombinant proteins. But only recently the advent of high-brilliance synchrotron sources, X-ray free-electron lasers, and improved serial data collection strategies has allowed the use of these micrometer-sized crystals for structural biology. Thus, in cellulo crystallization could offer exciting new possibilities for proteins that do not crystallize applying conventional approaches. In this review, we comprehensively summarize the current knowledge of intracellular protein crystallization. This includes an overview of the cellular functions, the physical properties, and, if known, the mode of regulation of native in cellulo crystal formation, complemented with a discussion of the reported crystallization events of recombinant proteins and the current method developments to successfully collect X-ray diffraction data from in cellulo crystals. Although the intracellular protein self-assembly mechanisms are still poorly understood, regulatory differences between native in cellulo crystallization linked to a specific function and accidently crystallizing proteins, either disease associated or recombinantly introduced, become evident. These insights are important to systematically exploit living cells as protein crystallization chambers in the future.
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Affiliation(s)
- Robert Schönherr
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, D-23562 Lübeck, Germany.,Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, D-22607 Hamburg, Germany
| | - Janine Mia Rudolph
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, D-23562 Lübeck, Germany.,Center for Free-Electron Laser Science (CFEL), DESY, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Lars Redecke
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, D-23562 Lübeck, Germany.,Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, D-22607 Hamburg, Germany
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9
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Molecular mechanisms of action of sphingomyelin-specific pore-forming toxin, lysenin. Semin Cell Dev Biol 2018; 73:188-198. [DOI: 10.1016/j.semcdb.2017.07.036] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 07/18/2017] [Accepted: 07/19/2017] [Indexed: 11/21/2022]
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10
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Yoshida C, Uchida Y, Ito T, Takami T, Murakami Y. Chitosan Gel Sheet Containing Polymeric Micelles: Synthesis and Gelation Properties of PEG-Grafted Chitosan. MATERIALS 2017; 10:ma10091075. [PMID: 28902160 PMCID: PMC5615729 DOI: 10.3390/ma10091075] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 09/12/2017] [Accepted: 09/12/2017] [Indexed: 01/06/2023]
Abstract
Wound-dressing sheet biomaterials can cover wound sites and enhance wound healing. In this study, a detailed evaluation of the factors affecting both the PEG modification percentage (PMP) in poly(ethylene glycol) (PEG)-grafted chitosan synthesis and the gelation properties of PEG-grafted chitosan was presented for constructing our novel hybrid hydrogel sheet consisting of PEG-grafted chitosan (a gel-forming polymer) and a reactive polymeric micelle (a crosslinker). It was confirmed that various factors (i.e., the weight ratio of PEG/chitosan, the pH of the buffer solution, reaction times, and reaction temperatures) in the preparation stage of PEG-grafted chitosans affected the PMP of PEG-grafted chitosans. Furthermore, the PMP of PEG-grafted chitosans affected their gelation properties. Finally, a ‘flexible’ hydrogel sheet that can be reversibly dried and moistened was successfully obtained. The dried rigid, thin sheet is expected to be suitable for stable preservation. The results obtained in this paper show that the incorporation of drug carriers into biomaterials is a novel approach to improve functionality.
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Affiliation(s)
- Chikara Yoshida
- Department of Organic and Polymer Materials Chemistry, Faculty of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
| | - Yusuke Uchida
- Department of Organic and Polymer Materials Chemistry, Faculty of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
| | - Tomoki Ito
- Department of Organic and Polymer Materials Chemistry, Faculty of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
| | - Taku Takami
- Department of Organic and Polymer Materials Chemistry, Faculty of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
| | - Yoshihiko Murakami
- Department of Organic and Polymer Materials Chemistry, Faculty of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
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11
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Liquid-liquid phase separation of a monoclonal antibody at low ionic strength: Influence of anion charge and concentration. Biophys Chem 2017; 220:7-19. [DOI: 10.1016/j.bpc.2016.08.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 08/20/2016] [Accepted: 08/20/2016] [Indexed: 12/15/2022]
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12
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Kellermeier M, Raiteri P, Berg JK, Kempter A, Gale JD, Gebauer D. Entropy Drives Calcium Carbonate Ion Association. Chemphyschem 2016; 17:3535-3541. [PMID: 27540706 DOI: 10.1002/cphc.201600653] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Indexed: 11/05/2022]
Abstract
The understanding of the molecular mechanisms underlying the early stages of crystallisation is still incomplete. In the case of calcium carbonate, experimental and computational evidence suggests that phase separation relies on so-called pre-nucleation clusters (PNCs). A thorough thermodynamic analysis of the enthalpic and entropic contributions to the overall free energy of PNC formation derived from three independent methods demonstrates that solute clustering is driven by entropy. This can be quantitatively rationalised by the release of water molecules from ion hydration layers, explaining why ion association is not limited to simple ion pairing. The key role of water release in this process suggests that PNC formation should be a common phenomenon in aqueous solutions.
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Affiliation(s)
| | - Paolo Raiteri
- Department of Chemistry, Curtin Institute for Computation and Institute for Geoscience Research, Curtin University, PO Box U1987, Perth, WA, 6845, Australia
| | - John K Berg
- Department of Chemistry, Physical Chemistry, University of Konstanz, Universitätsstraße 10, D-78464, Konstanz, Germany
| | - Andreas Kempter
- Reactive Systems and Inorganic Nanomaterials Research, BASF SE, D-67056, Ludwigshafen, Germany
| | - Julian D Gale
- Department of Chemistry, Curtin Institute for Computation and Institute for Geoscience Research, Curtin University, PO Box U1987, Perth, WA, 6845, Australia
| | - Denis Gebauer
- Department of Chemistry, Physical Chemistry, University of Konstanz, Universitätsstraße 10, D-78464, Konstanz, Germany
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13
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Raut AS, Kalonia DS. Pharmaceutical Perspective on Opalescence and Liquid–Liquid Phase Separation in Protein Solutions. Mol Pharm 2016; 13:1431-44. [DOI: 10.1021/acs.molpharmaceut.5b00937] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Ashlesha S. Raut
- Department of Pharmaceutical
Sciences, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Devendra S. Kalonia
- Department of Pharmaceutical
Sciences, University of Connecticut, Storrs, Connecticut 06269, United States
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14
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Raut AS, Kalonia DS. Liquid–Liquid Phase Separation in a Dual Variable Domain Immunoglobulin Protein Solution: Effect of Formulation Factors and Protein–Protein Interactions. Mol Pharm 2015; 12:3261-71. [DOI: 10.1021/acs.molpharmaceut.5b00256] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ashlesha S. Raut
- Department of Pharmaceutical
Sciences, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Devendra S. Kalonia
- Department of Pharmaceutical
Sciences, University of Connecticut, Storrs, Connecticut 06269, United States
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15
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Aich A, Pan W, Vekilov PG. Thermodynamic mechanism of free heme action on sickle cell hemoglobin polymerization. AIChE J 2015. [DOI: 10.1002/aic.14800] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Anupam Aich
- Department of Chemical and Biomolecular Engineering; University of Houston; Houston TX 77204
| | - Weichun Pan
- Department of Chemical and Biomolecular Engineering; University of Houston; Houston TX 77204
| | - Peter G. Vekilov
- Department of Chemical and Biomolecular Engineering; University of Houston; Houston TX 77204
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16
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Hekmat D. Large-scale crystallization of proteins for purification and formulation. Bioprocess Biosyst Eng 2015; 38:1209-31. [PMID: 25700885 DOI: 10.1007/s00449-015-1374-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 02/02/2015] [Indexed: 12/17/2022]
Abstract
Since about 170 years, salts were used to create supersaturated solutions and crystallize proteins. The dehydrating effect of salts as well as their kosmotropic or chaotropic character was revealed. Even the suitability of organic solvents for crystallization was already recognized. Interestingly, what was performed during the early times is still practiced today. A lot of effort was put into understanding the underlying physico-chemical interaction mechanisms leading to protein crystallization. However, it was understood that already the solvation of proteins is a highly complex process not to mention the intricate interrelation of electrostatic and hydrophobic interactions taking place. Although many basic questions are still unanswered, preparative protein crystallization was attempted as illustrated in the presented case studies. Due to the highly variable nature of crystallization, individual design of the crystallization process is needed in every single case. It was shown that preparative crystallization from impure protein solutions as a capture step is possible after applying adequate pre-treatment procedures like precipitation or extraction. Protein crystallization can replace one or more chromatography steps. It was further shown that crystallization can serve as an attractive alternative means for formulation of therapeutic proteins. Crystalline proteins can offer enhanced purity and enable highly concentrated doses of the active ingredient. Easy scalability of the proposed protein crystallization processes was shown using the maximum local energy dissipation as a suitable scale-up criterion. Molecular modeling and target-oriented protein engineering may allow protein crystallization to become part of a platform purification process in the near future.
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Affiliation(s)
- Dariusch Hekmat
- Institute of Biochemical Engineering, Technische Universität München, Boltzmannstr. 15, 85748, Garching, Germany,
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17
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Vekilov PG, Vorontsova MA. Nucleation precursors in protein crystallization. Acta Crystallogr F Struct Biol Commun 2014; 70:271-82. [PMID: 24598910 PMCID: PMC3944685 DOI: 10.1107/s2053230x14002386] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 02/02/2014] [Indexed: 11/10/2022] Open
Abstract
Protein crystal nucleation is a central problem in biological crystallography and other areas of science, technology and medicine. Recent studies have demonstrated that protein crystal nuclei form within crucial precursors. Here, methods of detection and characterization of the precursors are reviewed: dynamic light scattering, atomic force microscopy and Brownian microscopy. Data for several proteins provided by these methods have demonstrated that the nucleation precursors are clusters consisting of protein-dense liquid, which are metastable with respect to the host protein solution. The clusters are several hundred nanometres in size, the cluster population occupies from 10(-7) to 10(-3) of the solution volume, and their properties in solutions supersaturated with respect to crystals are similar to those in homogeneous, i.e. undersaturated, solutions. The clusters exist owing to the conformation flexibility of the protein molecules, leading to exposure of hydrophobic surfaces and enhanced intermolecular binding. These results indicate that protein conformational flexibility might be the mechanism behind the metastable mesoscopic clusters and crystal nucleation. Investigations of the cluster properties are still in their infancy. Results on direct imaging of cluster behaviors and characterization of cluster mechanisms with a variety of proteins will soon lead to major breakthroughs in protein biophysics.
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Affiliation(s)
- Peter G. Vekilov
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204-4004, USA
- Department of Chemistry, University of Houston, Houston, TX 77204-4004, USA
| | - Maria A. Vorontsova
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204-4004, USA
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18
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Giegé R. A historical perspective on protein crystallization from 1840 to the present day. FEBS J 2013; 280:6456-97. [DOI: 10.1111/febs.12580] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 08/30/2013] [Accepted: 09/27/2013] [Indexed: 12/22/2022]
Affiliation(s)
- Richard Giegé
- Institut de Biologie Moléculaire et Cellulaire; Université de Strasourg et CNRS; France
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19
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Ito T, Yoshida C, Murakami Y. Design of novel sheet-shaped chitosan hydrogel for wound healing: A hybrid biomaterial consisting of both PEG-grafted chitosan and crosslinkable polymeric micelles acting as drug containers. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2013; 33:3697-703. [DOI: 10.1016/j.msec.2013.04.056] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 04/22/2013] [Accepted: 04/27/2013] [Indexed: 10/26/2022]
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20
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Uskoković V. Revisiting the Fundamentals in the Design and Control of Nanoparticulate Colloids in the Frame of Soft Chemistry. REVIEW JOURNAL OF CHEMISTRY 2013; 3:271-303. [PMID: 24490052 PMCID: PMC3906689 DOI: 10.1134/s2079978013040031] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
This review presents thoughts on some of the fundamental features of conceptual models applied in the design of fine particles in the frames of colloid and soft chemistry. A special emphasis is placed on the limitations of these models, an acknowledgment of which is vital in improving their intricacy and effectiveness in predicting the outcomes of the corresponding experimental settings. Thermodynamics of self-assembly phenomena illustrated on the examples of protein assembly and micellization is analyzed in relation to the previously elaborated thesis that each self-assembly in reality presents a co-assembly, since it implies a mutual reorganization of the assembling system and its immediate environment. Parameters used in the design of fine particles by precipitation are discussed while referring to solubility product, various measures of supersaturation levels, induction time, nucleation and crystal growth rates, interfacial energies, and the Ostwald-Lussac law of phases. Again, the main drawbacks and inadequacies of using the aforementioned parameters in tailoring the materials properties in a soft and colloidal chemical setting were particularly emphasized. The basic and practical limitations of zeta-potential analyses, routinely used to stabilize colloidal dispersions and initiate specific interactions between soft chemical entities, were also outlined. The final section of the paper reiterates the unavoidable presence of practical qualitative models in the design and control of nanoparticulate colloids, which is supported by the overwhelming complexity of quantitative relationships that govern the processes of their formation and assembly.
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Affiliation(s)
- Vuk Uskoković
- Therapeutic Micro and Nanotechnology Laboratory, Department of Bioengineering and Therapeutic Sciences, University of California, 1700 4th Street, QB3 204, Mission Bay Campus, San Francisco, CA 94158-2330707, USA
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21
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Vekilov PG. Phase diagrams and kinetics of phase transitions in protein solutions. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2012; 24:193101. [PMID: 22495288 DOI: 10.1088/0953-8984/24/19/193101] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The phase behavior of proteins is of interest for fundamental and practical reasons. The nucleation of new phases is one of the last major unresolved problems of nature. The formation of protein condensed phases (crystals, polymers, and other solid aggregates, as well as dense liquids and gels) underlies pathological conditions, plays a crucial role in the biological function of the respective protein, or is an essential part of laboratory and industrial processes. In this review, we focus on phase transitions of proteins in their properly folded state. We first summarize the recently acquired understanding of physical processes underlying the phase diagrams of the protein solutions and the thermodynamics of protein phase transitions. Then we review recent findings on the kinetics of nucleation of dense liquid droplets and crystals. We explore the transition from nucleation to spinodal decomposition for liquid-liquid separation and introduce the new concept of solution-to-crystal spinodal. We review the two-step mechanism of protein crystal nucleation, in which mesoscopic metastable protein clusters serve as precursors to the ordered crystal nuclei. The concepts and mechanisms reviewed here provide powerful tools for control of the nucleation process by varying the solution thermodynamic parameters.
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Affiliation(s)
- Peter G Vekilov
- Department of Chemical and Biomolecular Engineering and Department of Chemistry, University of Houston, Houston, TX 77204-4004, USA.
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22
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Entropy-driven binding of opioid peptides induces a large domain motion in human dipeptidyl peptidase III. Proc Natl Acad Sci U S A 2012; 109:6525-30. [PMID: 22493238 DOI: 10.1073/pnas.1118005109] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Opioid peptides are involved in various essential physiological processes, most notably nociception. Dipeptidyl peptidase III (DPP III) is one of the most important enkephalin-degrading enzymes associated with the mammalian pain modulatory system. Here we describe the X-ray structures of human DPP III and its complex with the opioid peptide tynorphin, which rationalize the enzyme's substrate specificity and reveal an exceptionally large domain motion upon ligand binding. Microcalorimetric analyses point at an entropy-dominated process, with the release of water molecules from the binding cleft ("entropy reservoir") as the major thermodynamic driving force. Our results provide the basis for the design of specific inhibitors that enable the elucidation of the exact role of DPP III and the exploration of its potential as a target of pain intervention strategies.
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What can Mesoscopic LevelIN SITUObservations Teach us About Kinetics and Thermodynamics of Protein Crystallization? ADVANCES IN CHEMICAL PHYSICS 2012. [DOI: 10.1002/9781118309513.ch9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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24
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Uzunova V, Pan W, Lubchenko V, Vekilov PG. Control of the nucleation of sickle cell hemoglobin polymers by free hematin. Faraday Discuss 2012. [DOI: 10.1039/c2fd20058a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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25
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Banerjee PR, Puttamadappa SS, Pande A, Shekhtman A, Pande J. Increased hydrophobicity and decreased backbone flexibility explain the lower solubility of a cataract-linked mutant of γD-crystallin. J Mol Biol 2011; 412:647-59. [PMID: 21827768 DOI: 10.1016/j.jmb.2011.07.058] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Revised: 07/22/2011] [Accepted: 07/25/2011] [Indexed: 11/18/2022]
Abstract
A number of point mutations in γD-crystallin are associated with human cataract. The Pro23-to-Thr (P23T) mutation is perhaps the most common, is geographically widespread, and presents itself in a variety of phenotypes. It is therefore important to understand the molecular basis of lens opacity due to this mutation. In our earlier studies, we noted that P23T shows retrograde and sharply lowered solubility, most likely due to the emergence of hydrophobic patches involved in protein aggregation. Binding of 4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonate (Bis-ANS) dye (a probe commonly used for detecting surface hydrophobicity) competed with aggregation, suggesting that the residues involved in Bis-ANS binding are also involved in protein aggregation. Here, using NMR spectroscopy in conjunction with Bis-ANS binding, we identify three residues (Y16, D21, and Y50) in P23T that are involved in binding the dye. Furthermore, using (15)N NMR relaxation experiments, we show that, in the mutant protein, backbone fluctuations are restricted to the picosecond-to-nanosecond and microsecond timescales relative to the wild type. Our present studies specify the residues involved in these two pivotal characteristics of the mutant protein, namely increased surface hydrophobicity and restricted mobility of the protein backbone, which can explain the nucleation and further propagation of protein aggregates. Thus, we have now identified the residues in the P23T mutant that give rise to novel hydrophobic surfaces, as well as those regions of the protein backbone where fluctuations in different timescales are restricted, providing a comprehensive understanding of how lens opacity could result from this mutation.
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Affiliation(s)
- Priya R Banerjee
- Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA
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Sanamaría-Holek I, Gadomski A, Rubí JM. Controlling protein crystal growth rate by means of temperature. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2011; 23:235101. [PMID: 21613701 DOI: 10.1088/0953-8984/23/23/235101] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We have proposed a model to analyze the growth kinetics of lysozyme crystals/aggregates under non-isothermal conditions. The model was formulated through an analysis of the entropy production of the growth process which was obtained by taking into account the explicit dependence of the free energy on the temperature. We found that the growth process is coupled with temperature variations, resulting in a novel Soret-type effect. We identified the surface entropy of the crystal/aggregate as a decisive ingredient controlling the behavior of the average growth rate as a function of temperature. The behavior of the Gibbs free energy as a function of temperature is also analyzed. The agreement between theory and experiments is very good in the range of temperatures considered.
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Affiliation(s)
- I Sanamaría-Holek
- Institute of Mathematics and Physics, University of Technology and Life Sciences, PL-85796 Bydgoszcz, Poland.
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Pan W, Uzunova VV, Vekilov PG. Free heme in micromolar amounts enhances the attraction between sickle cell hemoglobin molecules. Biopolymers 2010; 91:1108-16. [PMID: 19322821 DOI: 10.1002/bip.21191] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We probe the role of free heme in the interactions between sickle cell hemoglobin (HbS) molecules in simulated physiological solutions: polymerization of deoxy-HbS is the primary pathogenic event of sickle cell anemia, and HbS releases heme after autoxidation more readily than normal adult hemoglobin. We characterize these interactions in terms of osmotic virial coefficients, which we determine by static light scattering. We analyze the results in the heme-hemoglobin system using the Kirkwood-Goldberg model. We show that in the absence of heme, the HbS molecules weakly attract and the attraction is not due to the lowered-as a result of the sickle cell mutation-molecular charge. We show that the part of the interface between the two alphabeta dimers, exposed in the deoxy-state, plays a crucial role in this attraction. We show that heme at micromolar concentrations induces strong attraction between the hemoglobin molecules. We show that the high efficacy of the heme results from the statistics of electrostatic and hydrophobic interactions between the heme and hemoglobin molecules.
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Affiliation(s)
- Weichun Pan
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204-4004, USA
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Canterino JE, Galkin O, Vekilov PG, Hirsch RE. Phase separation and crystallization of hemoglobin C in transgenic mouse and human erythrocytes. Biophys J 2008; 95:4025-33. [PMID: 18621841 PMCID: PMC2553125 DOI: 10.1529/biophysj.107.127324] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2007] [Accepted: 06/13/2008] [Indexed: 11/18/2022] Open
Abstract
Individuals expressing hemoglobin C (beta6 Glu-->Lys) present red blood cells (RBC) with intraerythrocytic crystals that form when hemoglobin (Hb) is oxygenated. Our earlier in vitro liquid-liquid (L-L) phase separation studies demonstrated that liganded HbC exhibits a stronger net intermolecular attraction with a longer range than liganded HbS or HbA, and that L-L phase separation preceded and enhanced crystallization. We now present evidence for the role of phase separation in HbC crystallization in the RBC, and the role of the RBC membrane as a nucleation center. RBC obtained from both human homozygous HbC patients and transgenic mice expressing only human HbC were studied by bright-field and differential interference contrast video-enhanced microscopy. RBC were exposed to hypertonic NaCl solution (1.5-3%) to induce crystallization within an appropriate experimental time frame. L-L phase separation occurred inside the RBC, which in turn enhanced the formation of intraerythrocytic crystals. RBC L-L phase separation and crystallization comply with the thermodynamic and kinetics laws established through in vitro studies of phase transformations. This is the first report, to the best of our knowledge, to capture a temporal view of intraerythrocytic HbC phase separation, crystal formation, and dissolution.
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Affiliation(s)
- Joseph E Canterino
- Department of Medicine and Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York, USA
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31
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Wentzel N, Gunton JD. Effect of Solvent on the Phase Diagram of a Simple Anisotropic Model of Globular Proteins. J Phys Chem B 2008; 112:7803-9. [DOI: 10.1021/jp801192p] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nathaniel Wentzel
- Department of Physics, Lehigh University, Bethlehem, Pennsylvania 18015
| | - James D. Gunton
- Department of Physics, Lehigh University, Bethlehem, Pennsylvania 18015
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32
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Derewenda ZS. Protein crystallization in drug design: towards a rational approach. Expert Opin Drug Discov 2007; 2:1329-40. [PMID: 23484529 DOI: 10.1517/17460441.2.10.1329] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
X-ray crystallography is the method of choice for the detailed characterization of stereochemistry of interactions of drug leads and potential chemotherapeutics with their protein targets. The resulting atomic models allow for rational enhancement of the lead properties and consequently for the design of high-affinity inhibitors. However, a major bottleneck of the technique is the requirement for the protein and its complexes to yield high quality single crystals. Furthermore, it is highly desirable that such crystals diffract to high resolution, preferably ≥ 1.2 Å, revealing the structures in atomic detail. Unfortunately, only a small portion of proteins readily crystallize in that fashion. New approaches are being developed to circumvent this problem. One proposed option includes rational protein surface engineering to systematically improve the crystallizability of the protein. This is accomplished by creating surface patches readily mediating weak, but specific, intermolecular interactions that take on the role of crystal contacts during nucleation and crystal growth phase.
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Affiliation(s)
- Zygmunt S Derewenda
- University of Virginia, Integrated Center for Structure and Function Innovation (PSI2), Departments of Molecular Physiology and Biological Physics, PO Box 800736, Jordan Hall, Charlottesville, VA 22908-0736, USA +1 434 243 6842 ; +1 434 982 1616 ;
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Gitlin I, Carbeck JD, Whitesides GM. Why are proteins charged? Networks of charge-charge interactions in proteins measured by charge ladders and capillary electrophoresis. Angew Chem Int Ed Engl 2007; 45:3022-60. [PMID: 16619322 DOI: 10.1002/anie.200502530] [Citation(s) in RCA: 196] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Almost all proteins contain charged amino acids. While the function in catalysis or binding of individual charges in the active site can often be identified, it is less clear how to assign function to charges beyond this region. Are they necessary for solubility? For reasons other than solubility? Can manipulating these charges change the properties of proteins? A combination of capillary electrophoresis (CE) and protein charge ladders makes it possible to study the roles of charged residues on the surface of proteins outside the active site. This method involves chemical modification of those residues to generate a large number of derivatives of the protein that differ in charge. CE separates those derivatives into groups with the same number of modified charged groups. By studying the influence of charge on the properties of proteins using charge ladders, it is possible to estimate the net charge and hydrodynamic radius and to infer the role of charged residues in ligand binding and protein folding.
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Affiliation(s)
- Irina Gitlin
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St., Cambridge, MA 02138, USA
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Doye JPK, Louis AA, Lin IC, Allen LR, Noya EG, Wilber AW, Kok HC, Lyus R. Controlling crystallization and its absence: proteins, colloids and patchy models. Phys Chem Chem Phys 2007; 9:2197-205. [PMID: 17487316 DOI: 10.1039/b614955c] [Citation(s) in RCA: 140] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The ability to control the crystallization behaviour (including its absence) of particles, be they biomolecules such as globular proteins, inorganic colloids, nanoparticles, or metal atoms in an alloy, is of both fundamental and technological importance. Much can be learnt from the exquisite control that biological systems exert over the behaviour of proteins, where protein crystallization and aggregation are generally suppressed, but where in particular instances complex crystalline assemblies can be formed that have a functional purpose. We also explore the insights that can be obtained from computational modelling, focussing on the subtle interplay between the interparticle interactions, the preferred local order and the resulting crystallization kinetics. In particular, we highlight the role played by "frustration", where there is an incompatibility between the preferred local order and the global crystalline order, using examples from atomic glass formers and model anisotropic particles.
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Affiliation(s)
- Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Oxford University, South Parks Road, Oxford, UK OX1 3QZ.
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35
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Pan W, Galkin O, Filobelo L, Nagel RL, Vekilov PG. Metastable mesoscopic clusters in solutions of sickle-cell hemoglobin. Biophys J 2006; 92:267-77. [PMID: 17040989 PMCID: PMC1697867 DOI: 10.1529/biophysj.106.094854] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Sickle cell hemoglobin (HbS) is a mutant, whose polymerization while in deoxy state in the venous circulation underlies the debilitating sickle cell anemia. It has been suggested that the nucleation of the HbS polymers occurs within clusters of dense liquid, existing in HbS solutions. We use dynamic light scattering with solutions of deoxy-HbS, and, for comparison, of oxy-HbS and oxy-normal adult hemoglobin, HbA. We show that solutions of all three Hb variants contain clusters of dense liquid, several hundred nanometers in size, which are metastable with respect to the Hb solutions. The clusters form within a few seconds after solution preparation and their sizes and numbers remain relatively steady for up to 3 h. The lower bound of the cluster lifetime is 15 ms. The clusters exist in broad temperature and Hb concentration ranges, and occupy 10(-5)-10(-2) of the solution volume. The results on the cluster properties can serve as test data for a potential future microscopic theory of cluster stability and kinetics. More importantly, if the clusters are a part of the nucleation mechanism of HbS polymers, the rate of HbS polymerization can be controlled by varying the cluster properties.
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Affiliation(s)
- Weichun Pan
- Department of Chemical Engineering, University of Houston, Houston, Texas 77204-4004, USA
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36
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Gitlin I, Carbeck JD, Whitesides GM. Warum sind Proteine geladen? Netzwerke aus Ladungs-Ladungs-Wechselwirkungen in Proteinen, analysiert über Ladungsleitern und Kapillarelektrophorese. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200502530] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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37
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Filobelo LF, Galkin O, Vekilov PG. Spinodal for the solution-to-crystal phase transformation. J Chem Phys 2005; 123:014904. [PMID: 16035866 DOI: 10.1063/1.1943413] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The formation of crystalline nuclei from solution has been shown for many systems to occur in two steps: the formation of quasidroplets of a disordered intermediate, followed by the nucleation of ordered crystalline embryos within these droplets. The rate of each step depends on a respective free-energy barrier and on the growth rate of its near-critical clusters. We address experimentally the relative significance of the free-energy barriers and the kinetic factors for the nucleation of crystals from solution using a model protein system. We show that crystal nucleation is 8-10 orders of magnitude slower than the nucleation of dense liquid droplets, i.e., the second step is rate determining. We show that at supersaturations of three or four k(B)T units, crystal nuclei of five, four, or three molecules transform into single-molecule nuclei, i.e., the significant nucleation barrier vanishes below the thermal energy of the molecules. We show that the main factor, which determines the rate of crystal nucleation, is the slow growth of the near-critical ordered clusters within the quasidroplets of the disordered intermediate. Analogous to the spinodal in supersaturated fluids, we define a solution-to-crystal spinodal from the transition to single-molecule crystalline nuclei. We show that heterogeneous nucleation centers accelerate nucleation not only because of the wettinglike effects that lower the nucleation barrier, as envisioned by classical theory, but by helping the kinetics of growth of the ordered crystalline embryos.
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Affiliation(s)
- Luis F Filobelo
- Department of Chemical Engineering, University of Houston, Houston, Texas 77204-4004, USA
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38
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Chen Q, Vekilov PG, Nagel RL, Hirsch RE. Liquid-liquid phase separation in hemoglobins: distinct aggregation mechanisms of the beta6 mutants. Biophys J 2004; 86:1702-12. [PMID: 14990498 PMCID: PMC1304006 DOI: 10.1016/s0006-3495(04)74239-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Reversible liquid-liquid (L-L) phase separation in the form of high concentration hemoglobin (Hb) solution droplets is favored in an equilibrium with a low-concentration Hb solution when induced by inositol-hexaphosphate in the presence of polyethylene glycol 4000 at pH 6.35 HEPES (50 mM). The L-L phase separation of Hb serves as a model to elucidate intermolecular interactions that may give rise to accelerated nucleation kinetics of liganded HbC (beta6 Lys) compared to HbS (beta6 Val) and HbA (beta6 Glu). Under conditions of low pH (pH 6.35) in the presence of inositol-hexaphosphate, COHb assumes an altered R-state. The phase lines for the three Hb variants in concentration and temperature coordinates indicate that liganded HbC exhibits a stronger net intermolecular attraction with a longer range than liganded HbS and HbA. Over time, L-L phase separation gives rise to amorphous aggregation and subsequent formation of crystals of different kinetics and habits, unique to the individual Hb. The composite of R- and T-like solution aggregation behavior indicates that this is a conformationally driven event. These results indicate that specific contact sites, thermodynamics, and kinetics all play a role in L-L phase separation and differ for the beta6 mutant hemoglobins compared to HbA. In addition, the dense liquid droplet interface or aggregate interface noticeably participates in crystal nucleation.
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Affiliation(s)
- Qiuying Chen
- Department of Medicine, Division of Hematology, Albert Einstein College of Medicine, Bronx, New York, USA
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39
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Feeling-Taylor AR, Yau ST, Petsev DN, Nagel RL, Hirsch RE, Vekilov PG. Crystallization mechanisms of hemoglobin C in the R state. Biophys J 2004; 87:2621-9. [PMID: 15454456 PMCID: PMC1304680 DOI: 10.1529/biophysj.104.039743] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2004] [Accepted: 06/16/2004] [Indexed: 11/18/2022] Open
Abstract
Crystallization of the mutated hemoglobin, HbC, which occurs inside red blood cells of patients expressing betaC-globin and exhibiting the homozygous CC and the heterozygous SC (in which two mutant beta-globins, S and C, are expressed) diseases, is a convenient model for processes underlying numerous condensation diseases. As a first step, we investigated the molecular-level mechanisms of crystallization of this protein from high-concentration phosphate buffer in its stable carbomonoxy form using high-resolution atomic force microscopy. We found that in conditions of equilibrium with the solution, the crystals' surface reconstructs into four-molecule-wide strands along the crystallographic a (or b) axis. However, the crystals do not grow by the alignment of such preformed strands. We found that the crystals grow by the attachment of single molecules to suitable sites on the surface. These sites are located along the edges of new layers generated by two-dimensional nucleation or by screw dislocations. During growth, the steps propagate with random velocities, with the mean being an increasing function of the crystallization driving force. These results show that the crystallization mechanisms of HbC are similar to those found for other proteins. Therefore, strategies developed to control protein crystallization in vitro may be applicable to pathology-related crystallization systems.
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Affiliation(s)
- Angela R Feeling-Taylor
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine and Montefiore Hospital, Comprehensive Sickle Cell Center, The Bronx, New York, USA
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40
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Bergeron L, Filobelo LF, Galkin O, Vekilov PG. Thermodynamics of the hydrophobicity in crystallization of insulin. Biophys J 2004; 85:3935-42. [PMID: 14645082 PMCID: PMC1303694 DOI: 10.1016/s0006-3495(03)74807-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
For insight into the solvent structure around protein molecules and its role in phase transformations, we investigate the thermodynamics of crystallization of the rhombohedral form of porcine insulin crystals. We determine the temperature dependence of the solubility at varying concentration of the co-solvent acetone, Cac=0%, 5%, 10%, 15%, and 20%, and find that, as a rule, the solubility of insulin increases as temperature increases. The enthalpy of crystallization, undergoes a stepwise shift from approximately -20 kJ mol(-1) at Cac=0%, 5%, and 10% to approximately -55 kJ mol(-1) at Cac=15% and 20%. The entropy change upon crystallization is approximately 35 J mol(-1) K(-1) for the first three acetone concentrations, and drops to approximately -110 J mol(-1) K(-1) at Cac=15% and 20%. DeltaS degrees cryst>0 indicates release of solvent, mostly water, molecules structured around the hydrophobic patches on the insulin molecules' surface in the solution. As Cac increases to 15% and above, unstructured acetone molecules apparently displace the waters and their contribution to DeltaS degrees cryst is minimal. This shifts DeltaS degrees cryst to a negative value close to the value expected for tying up of one insulin molecule from the solution. The accompanying increase in DeltaH degrees cryst suggests that the water structured around the hydrophobic surface moieties has a minimal enthalpy effect, likely due to the small size of these moieties. These findings provide values of the parameters needed to better control insulin crystallization, elucidate the role of organic additives in the crystallization of proteins, and help us to understand the thermodynamics of the hydrophobicity of protein molecules and other large molecules.
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Affiliation(s)
- Lisa Bergeron
- Department of Chemical Engineering, University of Houston, Houston, Texas 77204-4004, USA
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41
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Doye JPK, Louis AA, Vendruscolo M. Inhibition of protein crystallization by evolutionary negative design. Phys Biol 2004; 1:P9-13. [PMID: 16204814 DOI: 10.1088/1478-3967/1/1/p02] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Why are proteins so hard to crystallize? We propose an 'evolutionary negative design' principle to explain this difficulty. Proteins have evolved to avoid crystallization because crystallization compromises the viability of the cell. Evolutionary negative design is supported by much evidence in the literature, including the effect of mutations on the crystallizability of a protein, the correlations found in the properties of crystal contacts in bioinformatics databases, and the positive use of protein crystallization by bacteria and viruses.
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Affiliation(s)
- Jonathan P K Doye
- University Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW, UK.
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Galkin O, Vekilov PG. Mechanisms of Homogeneous Nucleation of Polymers of Sickle Cell Anemia Hemoglobin in Deoxy State. J Mol Biol 2004; 336:43-59. [PMID: 14741202 DOI: 10.1016/j.jmb.2003.12.019] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The primary pathogenic event of sickle cell anemia is the polymerization of the mutant hemoglobin (Hb) S within the red blood cells, occurring when HbS is in deoxy state in the venous circulation. Polymerization is known to start with nucleation of individual polymer fibers, followed by growth and branching via secondary nucleation, yet the mechanisms of nucleation of the primary fibers have never been subjected to dedicated tests. We implement a technique for direct determination of rates and induction times of primary nucleation of HbS fibers, based on detection of emerging HbS polymers using optical differential interference contrast microscopy after laser photolysis of CO-HbS. We show that: (i). nucleation throughout these determinations occurs homogeneously and not on foreign substrates; (ii). individual nucleation events are independent of each other; (iii). the nucleation rates are of the order of 10(6)-10(8)cm(-3)s(-1); (iv). nucleation induction times agree with an a priori prediction based on Zeldovich's theory; (v). in the probed parameter space, the nucleus contains 11 or 12 molecules. The nucleation rate values are comparable to those leading to erythrocyte sickling in vivo and suggest that the mechanisms deduced from in vitro experiments might provide physiologically relevant insights. While the statistics and dynamics of nucleation suggest mechanisms akin to those for small-molecule and protein crystals, the nucleation rate values are nine to ten orders of magnitude higher than those known for protein crystals. These high values cannot be rationalized within the current understanding of the nucleation processes.
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Affiliation(s)
- Oleg Galkin
- Department of Chemical Engineering, University of Houston, Houston, TX 77204-4004, USA
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Abstract
Homozygous HbC gene results only in mild hemolytic anemia. In HbSC disease red cells contain equal levels of HbS and HbC. It is a paradox that HbSC exhibit a moderately severe phenotype in spite of being a mixture of HbS trait and HbC trait, neither of which has significant pathology. Why does the combination of these two Hbs result in a serious disease? The short answer is that HbC enhances, by dehydrating the SC red cell, the pathogenic properties of HbS, resulting in a clinically significant disorder, but somewhat milder that sickle cell anemia (SCA). Nevertheless, retinnitis proliferans, osteonecrosis, and acute chest syndrome have equal or higher incidence in HbSC disease compared to SCA. This pathogenic trick is accomplished by HbC inducing, by mechanisms not fully understood, an increase in the activity of K:Cl cotransport that induces the lost of K(+) and consequently of intracellular water. This event creates a sufficient increase of MCHC, so that the lower levels of HbS found in SC red cells can polymerize rapidly and effectively. This situation offers a unique opportunity: if we could inhibit the effect of HbC on K(+) transport we can cure the disease.
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Affiliation(s)
- Ronald L Nagel
- Division of Hematology, Department of Medicine, Albert Einstein College of Medicine and Montefiore Medical Center, The Bronx, NY, USA
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Abstract
Static and dynamic light scattering are discussed as particularly useful tools for studying various aspects of protein crystal growth. Specific applications for prenucleation assays as well as for monitoring postnucleation growth processes are presented. Protein-protein interactions determined by light scattering, which serve as a predictor for favorable crystallization conditions as well as for protein solubility behavior, are detailed. Several precautions regarding the practical aspects of light scattering and interpretation of data are also discussed.
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Affiliation(s)
- W William Wilson
- Department of Chemistry, Mississippi State University, Box 9573, 39762, Mississippi State, MS, USA
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45
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Affiliation(s)
- Peter G Vekilov
- Department of Chemical Engineering, University of Houston, Houston, Texas 77204, USA
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