1
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Manning MC, Holcomb RE, Payne RW, Stillahn JM, Connolly BD, Katayama DS, Liu H, Matsuura JE, Murphy BM, Henry CS, Crommelin DJA. Stability of Protein Pharmaceuticals: Recent Advances. Pharm Res 2024; 41:1301-1367. [PMID: 38937372 DOI: 10.1007/s11095-024-03726-x] [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: 03/25/2024] [Accepted: 06/03/2024] [Indexed: 06/29/2024]
Abstract
There have been significant advances in the formulation and stabilization of proteins in the liquid state over the past years since our previous review. Our mechanistic understanding of protein-excipient interactions has increased, allowing one to develop formulations in a more rational fashion. The field has moved towards more complex and challenging formulations, such as high concentration formulations to allow for subcutaneous administration and co-formulation. While much of the published work has focused on mAbs, the principles appear to apply to any therapeutic protein, although mAbs clearly have some distinctive features. In this review, we first discuss chemical degradation reactions. This is followed by a section on physical instability issues. Then, more specific topics are addressed: instability induced by interactions with interfaces, predictive methods for physical stability and interplay between chemical and physical instability. The final parts are devoted to discussions how all the above impacts (co-)formulation strategies, in particular for high protein concentration solutions.'
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Affiliation(s)
- Mark Cornell Manning
- Legacy BioDesign LLC, Johnstown, CO, USA.
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA.
| | - Ryan E Holcomb
- Legacy BioDesign LLC, Johnstown, CO, USA
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
| | - Robert W Payne
- Legacy BioDesign LLC, Johnstown, CO, USA
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
| | - Joshua M Stillahn
- Legacy BioDesign LLC, Johnstown, CO, USA
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
| | | | | | | | | | | | - Charles S Henry
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
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2
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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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3
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Pereira AF, Martínez L. Helical Content Correlations and Hydration Structures of the Folding Ensemble of the B Domain of Protein A. J Chem Inf Model 2024; 64:3350-3359. [PMID: 38566451 DOI: 10.1021/acs.jcim.3c01822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The B domain of protein A (BdpA), a small three-helix bundle, folds on a time scale of a few microseconds with heterogeneous native and unfolded states. It is widely used as a model for understanding protein folding mechanisms. In this work, we use structure-based models (SBMs) and atomistic simulations to comprehensively investigate how BdpA folding is associated with the formation of its secondary structure. The energy landscape visualization method (ELViM) was used to characterize the pathways that connect the folded and unfolded states of BdpA as well as the sets of structures displaying specific ellipticity patterns. We show that the native state conformational diversity is due mainly to the conformational variability of helix I. Helices I, II, and III occur in a weakly correlated manner, with Spearman's rank correlation coefficients of 0.1539 (I and II), 0.1259 (I and III), and 0.2561 (II and III). These results, therefore, suggest the highest cooperativity between helices II and III. Our results allow the clustering of partially folded structures of folding of the B domain of protein A on the basis of its secondary structure, paving the way to an understanding of environmental factors in the relative stability of the basins of the folding ensemble, which are illustrated by the structural dependency of the protein hydration structures, as computed with minimum-distance distribution functions.
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Affiliation(s)
- Ander Francisco Pereira
- Institute of Chemistry and Center for Computing in Engineering & Science, Universidade Estadual de Campinas (UNICAMP), 13083-861 Campinas, SP, Brazil
| | - Leandro Martínez
- Institute of Chemistry and Center for Computing in Engineering & Science, Universidade Estadual de Campinas (UNICAMP), 13083-861 Campinas, SP, Brazil
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4
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Kumar A, Daschakraborty S. Anomalous lateral diffusion of lipids during the fluid/gel phase transition of a lipid membrane. Phys Chem Chem Phys 2023; 25:31431-31443. [PMID: 37962400 DOI: 10.1039/d3cp04081j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
A lipid membrane undergoes a phase transition from fluid to gel phase upon changing external thermodynamic conditions, such as decreasing temperature and increasing pressure. Extremophilic organisms face the challenge of preventing this deleterious phase transition. The main focus of their adaptive strategy is to facilitate effective temperature sensing through sensor proteins, relying on the drastic changes in packing density and membrane fluidity during the phase transition. Although the changes in packing density parameters due to the fluid/gel phase transition are studied in detail, the impact on membrane fluidity is less explored in the literature. Understanding the lateral diffusive dynamics of lipids in response to temperature, particularly during the fluid/gel phase transition, is albeit crucial. Here we have simulated the phase transition of a single component lipid membrane composed of dipalmitoylphosphatidylcholine (DPPC) lipids using a coarse-grained (CG) model and studied the changes of the structural and dynamical properties. It is observed that near the phase transition point, both fluid and gel phase domains coexist together. The dynamics remains highly non-Gaussian for a long time even when the mean square displacement reaches the Fickian regime at a much earlier time. This Fickian yet non-Gaussian diffusion (FnGD) is a characteristic of a highly heterogeneous system, previously observed for the lateral diffusion of lipids in raft mimetic membranes having liquid-ordered and liquid-disordered phases co-existing together. We have analyzed the molecular trajectories and calculated the jump-diffusion of the lipids, stemming from sudden jump translations, using a translational jump-diffusion (TJD) approach. An overwhelming contribution of the jump-diffusion of the lipids is observed suggesting anomalous diffusion of lipids during fluid/gel phase transition of the membrane. These results are important in unravelling the intricate nature of lipid diffusion during the phase transition of the membrane and open up a new possibility of investigating the most significant change of membrane properties during phase transition, which can be effectively sensed by proteins.
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Affiliation(s)
- Abhay Kumar
- Department of Chemistry, Indian Institute of Technology Patna, Bihar 801106, India.
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5
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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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6
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Shumilin I, Tanbuz A, Harries D. Deep Eutectic Solvents for Efficient Drug Solvation: Optimizing Composition and Ratio for Solubility of β-Cyclodextrin. Pharmaceutics 2023; 15:pharmaceutics15051462. [PMID: 37242704 DOI: 10.3390/pharmaceutics15051462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/30/2023] [Accepted: 05/07/2023] [Indexed: 05/28/2023] Open
Abstract
Deep eutectic solvents (DESs) show promise in pharmaceutical applications, most prominently as excellent solubilizers. Yet, because DES are complex multi-component mixtures, it is challenging to dissect the contribution of each component to solvation. Moreover, deviations from the eutectic concentration lead to phase separation of the DES, making it impractical to vary the ratios of components to potentially improve solvation. Water addition alleviates this limitation as it significantly decreases the melting temperature and stabilizes the DES single-phase region. Here, we follow the solubility of β-cyclodextrin (β-CD) in DES formed by the eutectic 2:1 mole ratio of urea and choline chloride (CC). Upon water addition to DES, we find that at almost all hydration levels, the highest β-CD solubility is achieved at DES compositions that are shifted from the 2:1 ratio. At higher urea to CC ratios, due to the limited solubility of urea, the optimum composition allowing the highest β-CD solubility is reached at the DES solubility limit. For mixtures with higher CC concentration, the composition allowing optimal solvation varies with hydration. For example, β-CD solubility at 40 wt% water is enhanced by a factor of 1.5 for a 1:2 urea to CC mole ratio compared with the 2:1 eutectic ratio. We further develop a methodology allowing us to link the preferential accumulation of urea and CC in the vicinity of β-CD to its increased solubility. The methodology we present here allows a dissection of solute interactions with DES components that is crucial for rationally developing improved drug and excipient formulations.
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Affiliation(s)
- Ilan Shumilin
- Institute of Chemistry, The Hebrew University, Jerusalem 9190401, Israel
- The Fritz Haber Research Center, The Hebrew University, Jerusalem 9190401, Israel
- The Harvey M. Krueger Family Center for Nanoscience and Nanotechnology, Edmond J. Safra Campus, The Hebrew University, Jerusalem 9190401, Israel
| | - Ahmad Tanbuz
- Institute of Chemistry, The Hebrew University, Jerusalem 9190401, Israel
- The Fritz Haber Research Center, The Hebrew University, Jerusalem 9190401, Israel
- The Harvey M. Krueger Family Center for Nanoscience and Nanotechnology, Edmond J. Safra Campus, The Hebrew University, Jerusalem 9190401, Israel
| | - Daniel Harries
- Institute of Chemistry, The Hebrew University, Jerusalem 9190401, Israel
- The Fritz Haber Research Center, The Hebrew University, Jerusalem 9190401, Israel
- The Harvey M. Krueger Family Center for Nanoscience and Nanotechnology, Edmond J. Safra Campus, The Hebrew University, Jerusalem 9190401, Israel
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7
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Shumilin I, Harries D. Enhanced solubilization in multi-component mixtures: mechanism of synergistic amplification of cyclodextrin solubility by urea and inorganic salts. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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8
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Maiti A, Kumar A, Daschakraborty S. How Do Cyclopropane Fatty Acids Protect the Cell Membrane of Escherichia coli in Cold Shock? J Phys Chem B 2023; 127:1607-1617. [PMID: 36790194 DOI: 10.1021/acs.jpcb.3c00541] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
The cyclopropanation of unsaturated lipid acyl chains of some bacterial cell membranes is an important survival strategy to protect the same against drastic cooling. To elucidate the role of cyclopropane ring-containing lipids, we have simulated the lipid membrane of Escherichia coli (E. coli) and two modified membranes by replacing the cyclopropane rings with either single or double bonds at widely different temperatures. It has been observed that the cyclopropane rings provide more rigid kinks in the lipid acyl chain compared to the double bonds and therefore further reduce the packing density of the membrane and subsequently enhance the membrane fluidity at low temperatures. They also inhibit the close packing of other lipids and deleterious phase separation by strongly interacting with them. Therefore, this study has explained why E. coli bacterial strain, susceptible to freezing environments, relies on the cyclopropanation of an unsaturated chain.
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Affiliation(s)
- Archita Maiti
- Department of Chemistry, Indian Institute of Technology Patna, Patna, Bihar 801106, India
| | - Abhay Kumar
- Department of Chemistry, Indian Institute of Technology Patna, Patna, Bihar 801106, India
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9
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Tian YM, Hofmann E, Silva W, Pu X, Touraud D, Gschwind RM, Kunz W, König B. Enforced Electronic-Donor-Acceptor Complex Formation in Water for Photochemical Cross-Coupling. Angew Chem Int Ed Engl 2023; 62:e202218775. [PMID: 36735337 DOI: 10.1002/anie.202218775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/02/2023] [Accepted: 02/03/2023] [Indexed: 02/04/2023]
Abstract
The amino alcohol meglumine solubilizes organic compounds in water and enforces the formation of electron donor acceptor (EDA) complexes of haloarenes with indoles, anilines, anisoles or thiols, which are not observed in organic solvents. UV-A photoinduced electron transfer within the EDA complexes induces the mesolytic cleavage of the halide ion and radical recombination of the arenes leading, after rearomatization and proton loss to C-C or C-S coupling products. Depending on the substitution pattern selective and unique cross-couplings are observed. UV and NMR measurements reveal the importance of the assembly for the photoinduced reaction. Enforced EDA aggregate formation in water allows new activation modes for organic photochemical synthesis.
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Affiliation(s)
- Ya-Ming Tian
- Faculty of Chemistry and Pharmacy, Institute of Organic Chemistry, University Regensburg, 93040, Regensburg, Germany
| | - Evamaria Hofmann
- Faculty of Chemistry and Pharmacy, Institute of Physical and Theoretical Chemistry, University Regensburg, 93040, Regensburg, Germany
| | - Wagner Silva
- Faculty of Chemistry and Pharmacy, Institute of Organic Chemistry, University Regensburg, 93040, Regensburg, Germany
| | - Xiang Pu
- Faculty of Chemistry and Pharmacy, Institute of Organic Chemistry, University Regensburg, 93040, Regensburg, Germany
| | - Didier Touraud
- Faculty of Chemistry and Pharmacy, Institute of Physical and Theoretical Chemistry, University Regensburg, 93040, Regensburg, Germany
| | - Ruth M Gschwind
- Faculty of Chemistry and Pharmacy, Institute of Organic Chemistry, University Regensburg, 93040, Regensburg, Germany
| | - Werner Kunz
- Faculty of Chemistry and Pharmacy, Institute of Physical and Theoretical Chemistry, University Regensburg, 93040, Regensburg, Germany
| | - Burkhard König
- Faculty of Chemistry and Pharmacy, Institute of Organic Chemistry, University Regensburg, 93040, Regensburg, Germany
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10
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Knop JM, Mukherjee S, Jaworek MW, Kriegler S, Manisegaran M, Fetahaj Z, Ostermeier L, Oliva R, Gault S, Cockell CS, Winter R. Life in Multi-Extreme Environments: Brines, Osmotic and Hydrostatic Pressure─A Physicochemical View. Chem Rev 2023; 123:73-104. [PMID: 36260784 DOI: 10.1021/acs.chemrev.2c00491] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Elucidating the details of the formation, stability, interactions, and reactivity of biomolecular systems under extreme environmental conditions, including high salt concentrations in brines and high osmotic and high hydrostatic pressures, is of fundamental biological, astrobiological, and biotechnological importance. Bacteria and archaea are able to survive in the deep ocean or subsurface of Earth, where pressures of up to 1 kbar are reached. The deep subsurface of Mars may host high concentrations of ions in brines, such as perchlorates, but we know little about how these conditions and the resulting osmotic stress conditions would affect the habitability of such environments for cellular life. We discuss the combined effects of osmotic (salts, organic cosolvents) and hydrostatic pressures on the structure, stability, and reactivity of biomolecular systems, including membranes, proteins, and nucleic acids. To this end, a variety of biophysical techniques have been applied, including calorimetry, UV/vis, FTIR and fluorescence spectroscopy, and neutron and X-ray scattering, in conjunction with high pressure techniques. Knowledge of these effects is essential to our understanding of life exposed to such harsh conditions, and of the physical limits of life in general. Finally, we discuss strategies that not only help us understand the adaptive mechanisms of organisms that thrive in such harsh geological settings but could also have important ramifications in biotechnological and pharmaceutical applications.
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Affiliation(s)
- Jim-Marcel Knop
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, D-44221Dortmund, Germany
| | - Sanjib Mukherjee
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, D-44221Dortmund, Germany
| | - Michel W Jaworek
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, D-44221Dortmund, Germany
| | - Simon Kriegler
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, D-44221Dortmund, Germany
| | - Magiliny Manisegaran
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, D-44221Dortmund, Germany
| | - Zamira Fetahaj
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, D-44221Dortmund, Germany
| | - Lena Ostermeier
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, D-44221Dortmund, Germany
| | - Rosario Oliva
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, D-44221Dortmund, Germany.,Department of Chemical Sciences, University of Naples Federico II, Via Cintia 4, 80126Naples, Italy
| | - Stewart Gault
- UK Centre for Astrobiology, SUPA School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, EH9 3FDEdinburgh, United Kingdom
| | - Charles S Cockell
- UK Centre for Astrobiology, SUPA School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, EH9 3FDEdinburgh, United Kingdom
| | - Roland Winter
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, D-44221Dortmund, Germany
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11
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Pereira AF, Piccoli V, Martínez L. Trifluoroethanol direct interactions with protein backbones destabilize α-helices. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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12
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Piccoli V, Martínez L. Ionic liquid solvation of proteins in native and denatured states. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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13
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TMAO to the rescue of pathogenic protein variants. Biochim Biophys Acta Gen Subj 2022; 1866:130214. [PMID: 35902028 DOI: 10.1016/j.bbagen.2022.130214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 07/11/2022] [Accepted: 07/21/2022] [Indexed: 11/22/2022]
Abstract
Trimethylamine N-oxide (TMAO) is a chemical chaperone found in various organisms including humans. Various studies unveiled that it is an excellent protein-stabilizing agent, and induces folding of unstructured proteins. It is also well established that it can counteract the deleterious effects of urea, salt, and hydrostatic pressure on macromolecular integrity. There is also existence of large body of data regarding its ability to restore functional deficiency of various mutant proteins or pathogenic variants by correcting misfolding defects and inhibiting the formation of high-order toxic protein oligomers. Since an important class of human disease called "protein conformational disorders" is due to protein misfolding and/or formation of high-order oligomers, TMAO stands as a promising molecule for the therapeutic intervention of such diseases. The present review has been designed to gather a comprehensive knowledge of the TMAO's effect on the functional restoration of various mutants, identify its shortcomings and explore its potentiality as a lead molecule. Future prospects have also been suitably incorporated.
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14
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Maiti A, Daschakraborty S. Can Urea and Trimethylamine- N-oxide Prevent the Pressure-Induced Phase Transition of Lipid Membrane? J Phys Chem B 2022; 126:1426-1440. [PMID: 35139638 DOI: 10.1021/acs.jpcb.1c08891] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Organisms dwelling in ocean trenches are exposed to the high hydrostatic pressure of ocean water. Increasing pressure can alter the membrane packing density and fluidity and trigger the fluid-to-gel phase transition. To combat environmental stress, the organisms synthesize small polar solutes, which are known as osmolytes. Urea and trimethylamine-N-oxide (TMAO) are two such solutes found in deep-sea creatures. While TMAO stabilizes protein, urea induces protein denaturation. These solutes strongly influence the packing density and membrane fluidity of the lipid bilayer at different conditions. But can these solutes affect the pressure-induced phase transition of the lipid membrane? In the present work, we have studied the effect of these two solutes on pressure-induced fluid-to-gel phase transition based on the all-atom molecular dynamics (MD) simulation approach. A high-pressure-stimulated fluid-to-gel phase transition of the membrane is seen at 800 bar, which is consistent with previous experiments. We have also observed that in the low-pressure region (1-400 bar), urea slightly increases the membrane fluidity where TMAO decreases the same. However, the phase transition pressure remains almost unchanged on the addition of urea while TMAO shifts the phase transition toward a lower pressure. We have found that the hydrogen (H)-bond interaction between lipid and urea plays an important role in preserving the fluidity of the membrane in the low-pressure zone. However, at a higher pressure, both water and urea are excluded from the membrane surface. TMAO is also excluded from the interfacial region of the membrane at all pressures. Exclusion from the membrane surface further triggers the phase transition of the lipid membrane from the fluid to gel phase at a high pressure.
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Affiliation(s)
- Archita Maiti
- Department of Chemistry, Indian Institute of Technology Patna, Bihar 801106, India
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15
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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: 40] [Impact Index Per Article: 20.0] [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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16
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Liu X, Stenhammar J, Wennerström H, Sparr E. Vesicles Balance Osmotic Stress with Bending Energy That Can Be Released to Form Daughter Vesicles. J Phys Chem Lett 2022; 13:498-507. [PMID: 35005979 PMCID: PMC8785185 DOI: 10.1021/acs.jpclett.1c03369] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/28/2021] [Indexed: 06/14/2023]
Abstract
The bending energy of the lipid membrane is central to biological processes involving vesicles, such as endocytosis and exocytosis. To illustrate the role of bending energy in these processes, we study the response of single-component giant unilamellar vesicles (GUVs) subjected to external osmotic stress by glucose addition. For osmotic pressures exceeding 0.15 atm, an abrupt shape change from spherical to prolate occurs, showing that the osmotic pressure is balanced by the free energy of membrane bending. After equilibration, the external glucose solution was exchanged for pure water, yielding rapid formation of monodisperse daughter vesicles inside the GUVs through an endocytosis-like process. Our theoretical analysis shows that this process requires significant free energies stored in the deformed membrane to be kinetically allowed. The results indicate that bending energies stored in GUVs are much higher than previously implicated, with potential consequences for vesicle fusion/fission and the osmotic regulation in living cells.
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Affiliation(s)
- Xiaoyan Liu
- Physical Chemistry, Lund University, 221 00 Lund, Sweden
| | | | | | - Emma Sparr
- Physical Chemistry, Lund University, 221 00 Lund, Sweden
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17
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Miranda-Quintana RA, Smiatek J. Electronic Properties of Protein Destabilizers and Stabilizers: Implications for Preferential Binding and Exclusion Mechanisms. J Phys Chem B 2021; 125:11857-11868. [PMID: 34672590 DOI: 10.1021/acs.jpcb.1c06295] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We study the electronic properties of low-weight organic co-solutes by means of conceptual density functional theory calculations. Our results highlight the important role of certain chemical reactivity descriptors such as chemical hardness, electronegativity, nucleofugality, and the electrofugality as important criteria to classify protein stabilizers and destabilizers. Our results imply Lewis basic properties with lower chemical hardness for stabilizers, while destabilizers show higher Lewis acidity with higher chemical hardness. Further consideration of analytical calculations in terms of transfer energies reveals the crucial role of co-solute-protein interactions which significantly change the interaction pattern of the stabilizing or destabilizing species. The corresponding outcomes connect statistical thermodynamics with the electronic properties of co-solutes and also allow us to define general principles for strong stabilizers and destabilizers.
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Affiliation(s)
- Ramón Alain Miranda-Quintana
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, Florida 32611, United States
| | - Jens Smiatek
- Institute for Computational Physics, University of Stuttgart, D-70569 Stuttgart, Germany
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18
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Keller F, Heuer A, Galla HJ, Smiatek J. Stabilization of DPPC lipid bilayers in the presence of co-solutes: molecular mechanisms and interaction patterns. Phys Chem Chem Phys 2021; 23:22936-22946. [PMID: 34622252 DOI: 10.1039/d1cp03052c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We study the interactions between dipalmitoylphosphatidylcholine (DPPC) lipid bilayers in the gel and the fluid phase with ectoine, amino ectoine and water molecules by means of atomistic molecular dynamics (MD) simulations and conceptual density functional theory (DFT) calculations. Our results reveal a pronounced preferential exclusion of both co-solutes from the DPPC lipid bilayer which is stronger for the fluid phase. The corresponding outcomes can be brought into relation with the Kirkwood-Buff theory of solutions in order to provide a thermodynamic rationale for the experimentally observed stabilization of the gel phase. Closely related to preferential exclusion of both co-solutes, our simulations also highlight a preferential hydration behavior as manifested by an increased number of hydrogen bonds between water and DPPC molecules. All results are rationalized by conceptual DFT calculations with regard to differences in the electronic properties between ectoine and amino ectoine.
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Affiliation(s)
- Fabian Keller
- Institute of Physical Chemistry, University of Münster, D-48149 Münster, Germany
| | - Andreas Heuer
- Institute of Physical Chemistry, University of Münster, D-48149 Münster, Germany
| | - Hans-Joachim Galla
- Institute of Biochemistry, University of Münster, D-48149 Münster, Germany
| | - Jens Smiatek
- Institute for Computational Physics, University of Stuttgart, D-70569 Stuttgart, Germany.
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19
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Maiti A, Daschakraborty S. How Do Urea and Trimethylamine N-Oxide Influence the Dehydration-Induced Phase Transition of a Lipid Membrane? J Phys Chem B 2021; 125:10149-10165. [PMID: 34486370 DOI: 10.1021/acs.jpcb.1c05852] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Living organisms are often exposed to extreme dehydration, which is detrimental to the structure and function of the cell membrane. The lipid membrane undergoes fluid-to-gel phase transition due to dehydration and thus loses fluidity and functionality. To protect the fluid phase of the bilayer these organisms adopt several strategies. Enhanced production of small polar organic solutes (also called osmolytes) is one such strategy. Urea and trimethylamine N-oxide (TMAO) are two osmolytes found in different organisms combating osmotic stress. Previous experiments have found that both these osmolytes have strong effects on lipid membrane under different hydration conditions. Urea prevents the dehydration-induced phase transition of the lipid membrane by directly interacting with the lipids, while TMAO does not inhibit the phase transition. To provide atomistic insights, we have carried out all-atom molecular dynamics (MD) simulation of a lipid membrane under varying hydration levels and studied the effect of these osmolytes on different structural and dynamic properties of the membrane. This study suggests that urea significantly inhibits the dehydration-induced fluid-to-gel phase transition by strongly interacting with the lipid membrane via hydrogen bonds, which balances the reduced lipid hydration due to the decreasing water content. In contrast, TMAO is excluded from the membrane surface due to unfavorable interaction with the lipids. This induces further dehydration of the lipids which reinforces the fluid-to-gel phase transition. We have also studied the counteractive role of TMAO on the effect of urea on lipid membrane when both the osmolytes are present. TMAO draws some urea molecules out of the membrane and thereby reduces the effect of urea on the lipid membrane at lower hydration levels. This is similar to the counteraction of urea's deleterious effects on protein by TMAO. All these observations are consistent with the experimental results and thus provide deep molecular insights into the role of these osmolytes in protecting the fluid phase of the membrane, the key survival strategy against osmotic-stress-induced dehydration.
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Affiliation(s)
- Archita Maiti
- Department of Chemistry, Indian Institute of Technology Patna, Bihar 801106, India
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20
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Pengyu Z, Yang Y, Ling Z, Jian G, Bing W, Xin B, Dehui Y, Linlin L, Congyu L, Na Z. The effect of trehalose on the thermodynamic stability and emulsification of soybean 11S globulin in the molten globule state. Food Hydrocoll 2021. [DOI: 10.1016/j.foodhyd.2021.106811] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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21
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Biochemical and structural studies of target lectin SapL1 from the emerging opportunistic microfungus Scedosporium apiospermum. Sci Rep 2021; 11:16109. [PMID: 34373510 PMCID: PMC8352872 DOI: 10.1038/s41598-021-95008-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 07/16/2021] [Indexed: 12/25/2022] Open
Abstract
Scedosporium apiospermum is an emerging opportunistic fungal pathogen responsible for life-threatening infections in humans. Host-pathogen interactions often implicate lectins that have become therapeutic targets for the development of carbohydrate mimics for antiadhesive therapy. Here, we present the first report on the identification and characterization of a lectin from S. apiospermum named SapL1. SapL1 was found using bioinformatics as a homolog to the conidial surface lectin FleA from Aspergillus fumigatus known to play a role in the adhesion to host glycoconjugates present in human lung epithelium. In our strategy to obtain recombinant SapL1, we discovered the importance of osmolytes to achieve its expression in soluble form in bacteria. Analysis of glycan arrays indicates specificity for fucosylated oligosaccharides as expected. Submicromolar affinity was measured for fucose using isothermal titration calorimetry. We solved SapL1 crystal structure in complex with α-methyl-L-fucoside and analyzed its structural basis for fucose binding. We finally demonstrated that SapL1 binds to bronchial epithelial cells in a fucose-dependent manner. The information gathered here will contribute to the design and development of glycodrugs targeting SapL1.
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22
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Ernst M, Robertson JL. The Role of the Membrane in Transporter Folding and Activity. J Mol Biol 2021; 433:167103. [PMID: 34139219 PMCID: PMC8756397 DOI: 10.1016/j.jmb.2021.167103] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 12/23/2022]
Abstract
The synthesis, folding, and function of membrane transport proteins are critical factors for defining cellular physiology. Since the stability of these proteins evolved amidst the lipid bilayer, it is no surprise that we are finding that many of these membrane proteins demonstrate coupling of their structure or activity in some way to the membrane. More and more transporter structures are being determined with some information about the surrounding membrane, and computational modeling is providing further molecular details about these solvation structures. Thus, the field is moving towards identifying which molecular mechanisms - lipid interactions, membrane perturbations, differential solvation, and bulk membrane effects - are involved in linking membrane energetics to transporter stability and function. In this review, we present an overview of these mechanisms and the growing evidence that the lipid bilayer is a major determinant of the fold, form, and function of membrane transport proteins in membranes.
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Affiliation(s)
- Melanie Ernst
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. Louis, 660 South Euclid Avenue, St. Louis, MO 63110, USA
| | - Janice L Robertson
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. Louis, 660 South Euclid Avenue, St. Louis, MO 63110, USA.
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23
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Shumilin I, Harries D. Cyclodextrin solubilization in hydrated reline: Resolving the unique stabilization mechanism in a deep eutectic solvent. J Chem Phys 2021; 154:224505. [PMID: 34241212 DOI: 10.1063/5.0052537] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
By complexing with hydrophobic compounds, cyclodextrins afford increased solubility and thermodynamic stability to hardly soluble compounds, thereby underlining their invaluable applications in pharmaceutical and other industries. However, common cyclodextrins such as β-cyclodextrin, suffer from limited solubility in water, which often leads to precipitation and formation of unfavorable aggregates, driving the search for better solvents. Here, we study the solvation of cyclodextrin in deep eutectic solvents (DESs), environmentally friendly media that possess unique properties. We focus on reline, the DES formed from choline chloride and urea, and resolve the mechanism through which its constituents elevate β-cyclodextrin solubility in hydrated solutions compared to pure water or dry reline. Combining experiments and simulations, we determine that the remarkable solubilization of β-cyclodextrin in hydrated reline is mostly due to the inclusion of urea inside β-cyclodextrin's cavity and at its exterior surfaces. The role of choline chloride in further increasing solvation is twofold. First, it increases urea's solubility beyond the saturation limit in water, ultimately leading to much higher β-cyclodextrin solubility in hydrated reline in comparison to aqueous urea solutions. Second, choline chloride increases urea's accumulation in β-cyclodextrin's vicinity. Specifically, we find that the accumulation of urea becomes stronger at high reline concentrations, as the solution transitions from reline-in-water to water-in-reline, where water alone cannot be regarded as the solvent. Simulations further suggest that in dry DES, the mechanism of β-cyclodextrin solvation changes so that reline acts as a quasi-single component solvent that lacks preference for the accumulation of urea or choline chloride around β-cyclodextrin.
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Affiliation(s)
- Ilan Shumilin
- The Fritz Haber Research Center, and The Harvey M. Krueger Family Center for Nanoscience and Nanotechnology, Edmond J. Safra Campus, Institute of Chemistry, The Hebrew University, Jerusalem 9190401, Israel
| | - Daniel Harries
- The Fritz Haber Research Center, and The Harvey M. Krueger Family Center for Nanoscience and Nanotechnology, Edmond J. Safra Campus, Institute of Chemistry, The Hebrew University, Jerusalem 9190401, Israel
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24
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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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25
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Treatment experience in two adults with creatinfe transporter deficiency. Mol Genet Metab Rep 2021; 27:100731. [PMID: 33665121 PMCID: PMC7907527 DOI: 10.1016/j.ymgmr.2021.100731] [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: 12/08/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 01/08/2023] Open
Abstract
Background Creatine transporter deficiency (CTD) is an X-linked form of intellectual disability (ID) caused by SCL6A8 mutations. Limited information exists on the adult course of CTD, and there are no treatment studies in adults. Methods We report two half-brothers with CTD, 36 and 31 years at intervention start. Their clinical phenotypes were consistent with CTD, and intervention was indicated because of progressive disease course, with increased difficulties speaking, walking and eating, resulting in fatigue, and malnutrition. We therefore performed treatment trials with arginine, glycine and a proprietary product containing creatine and betaine, and then a trial supplementing with betaine alone. Results In the older patient, glycine and arginine were accompanied by adverse effects, while betaine containing proprietary product gave improved balance, speech and feeding. When supplementation stopped, his condition deteriorated, and improved again after starting betaine supplement. Betaine supplementation was also beneficial in the younger patient, reducing his exhaustion, feeding difficulties and weight loss, making him able to resume his protected work. Discussion & conclusion We report for the first time that betaine supplement was well tolerated and efficient in adults with CTD, while arginine and/or glycine were accompanied by side effects. Thus, betaine is potentially a new useful treatment for CTD patients. We discuss possible underlying treatment mechanisms. Betaine has been reported to have antagonistic effect on NKCC1 channels, a mechanism shared with bumetanide, a medication with promising results in both in autism and epilepsy. Further studies of betaine's effects in well-designed studies are warranted.
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26
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Moses D, Yu F, Ginell GM, Shamoon NM, Koenig PS, Holehouse AS, Sukenik S. Revealing the Hidden Sensitivity of Intrinsically Disordered Proteins to their Chemical Environment. J Phys Chem Lett 2020; 11:10131-10136. [PMID: 33191750 PMCID: PMC8092420 DOI: 10.1021/acs.jpclett.0c02822] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Intrinsically disordered protein-regions (IDRs) make up roughly 30% of the human proteome and are central to a wide range of biological processes. Given a lack of persistent tertiary structure, all residues in IDRs are, to some extent, solvent exposed. This extensive surface area, coupled with the absence of strong intramolecular contacts, makes IDRs inherently sensitive to their chemical environment. We report a combined experimental, computational, and analytical framework for high-throughput characterization of IDR sensitivity. Our framework reveals that IDRs can expand or compact in response to changes in their solution environment. Importantly, the direction and magnitude of conformational change depend on both protein sequence and cosolute identity. For example, some solutes such as short polyethylene glycol chains exert an expanding effect on some IDRs and a compacting effect on others. Despite this complex behavior, we can rationally interpret IDR responsiveness to solution composition changes using relatively simple polymer models. Our results imply that solution-responsive IDRs are ubiquitous and can provide an additional layer of regulation to biological systems.
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Affiliation(s)
- David Moses
- Chemistry and Chemical Biology Program, University of California, Merced, CA
- Center for Cellular and Biomolecular Machines (CCBM), University of California, Merced, CA
| | - Feng Yu
- Center for Cellular and Biomolecular Machines (CCBM), University of California, Merced, CA
- Quantitative Systems Biology Program, University of California, Merced, CA
| | - Garrett M. Ginell
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO
| | | | - Patrick S. Koenig
- Quantitative Systems Biology Program, University of California, Merced, CA
| | - Alex S. Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO
| | - Shahar Sukenik
- Chemistry and Chemical Biology Program, University of California, Merced, CA
- Center for Cellular and Biomolecular Machines (CCBM), University of California, Merced, CA
- Quantitative Systems Biology Program, University of California, Merced, CA
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27
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Piccoli V, Martínez L. Correlated counterion effects on the solvation of proteins by ionic liquids. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.114347] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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28
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Assessing the role of osmolytes on the conformational harmony of islet amyloid polypeptide. Int J Biol Macromol 2020; 164:2569-2582. [DOI: 10.1016/j.ijbiomac.2020.08.104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 08/05/2020] [Accepted: 08/11/2020] [Indexed: 02/07/2023]
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29
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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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30
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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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31
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de Oliveira IP, Martínez L. The shift in urea orientation at protein surfaces at low pH is compatible with a direct mechanism of protein denaturation. Phys Chem Chem Phys 2020; 22:354-367. [DOI: 10.1039/c9cp05196a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The protonation of acidic side-chains promotes a orientational shift of urea molecules, but only locally, with the interactions with other protein moieties being preserved.
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Affiliation(s)
- Ivan Pires de Oliveira
- Institute of Chemistry and Center for Computing in Engineering & Science
- University of Campinas
- Campinas
- Brazil
- Department of Pharmacology
| | - Leandro Martínez
- Institute of Chemistry and Center for Computing in Engineering & Science
- University of Campinas
- Campinas
- Brazil
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32
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Jahan I, Nayeem SM. Effect of Osmolytes on Conformational Behavior of Intrinsically Disordered Protein α-Synuclein. Biophys J 2019; 117:1922-1934. [PMID: 31699336 DOI: 10.1016/j.bpj.2019.09.046] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 09/21/2019] [Accepted: 09/30/2019] [Indexed: 11/20/2022] Open
Abstract
α-Synuclein is an intrinsically disordered protein whose function in a healthy brain is poorly understood. It is genetically and neuropathologically linked to Parkinson's disease (PD). PD is manifested after the accumulation of plaques of α-synuclein aggregates in the brain cells. Aggregates of α-synuclein are very toxic and lead to the disruption of cellular homeostasis and neuronal death. α-Synuclein can also contribute to disease propagation as it may exert noxious effects on neighboring cells. Understanding the mechanism of α-synuclein aggregation will facilitate the problem of dealing with neurodegenerative diseases in general and that of PD in particular. Here, we have used molecular dynamics simulations to investigate the behavior of α-synuclein at various temperatures and in different concentrations of urea and trimethyl amine oxide. The residue region from 61 to 95 of α-synuclein is experimentally known as amyloidogenic. In our study, we have identified some other regions, which also have the propensity to form an aggregate besides this known sequence. Urea being a denaturant interacts more with these regions of α-synuclein through hydrogen bond formation and inhibits the β-sheet formation, whereas trimethyl amine oxide itself does not interact much with the protein and stabilizes the protein by preferentially distributing water molecules on the surface of the protein.
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Affiliation(s)
- Ishrat Jahan
- Department of Chemistry, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Shahid M Nayeem
- Department of Chemistry, Aligarh Muslim University, Aligarh, Uttar Pradesh, India.
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33
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Fedotova MV. Compatible osmolytes - bioprotectants: Is there a common link between their hydration and their protective action under abiotic stresses? J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111339] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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34
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Banks DD, Cordia JF, Spasojevic V, Sun J, Franc S, Cho Y. Isotonic concentrations of excipients control the dimerization rate of a therapeutic immunoglobulin G1 antibody during refrigerated storage based on their rank order of native-state interaction. Protein Sci 2019; 27:2073-2083. [PMID: 30267438 DOI: 10.1002/pro.3518] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 09/06/2018] [Accepted: 09/25/2018] [Indexed: 01/12/2023]
Abstract
Inert co-solutes, or excipients, are often included in protein biologic formulations to adjust the tonicity of liquid dosage forms intended for subcutaneous delivery. Despite the low concentration of their use, many of these excipients alter protein-protein interactions such as dimerization and aggregation rates of high concentration monoclonal antibody (mAb) therapeutics to varying extents during long-term refrigerated clinical storage, challenging the formulation scientist to make informed excipient selections at the earliest stages of development when protein supply and time are often limited. The objectives of this study were to better understand how isotonic concentrations of excipients influence the dimerization rates of a model mAb stored at refrigerated and room temperatures and explore protein sparing biophysical methods capable of predicting this dependence. Despite their prevalence of use in the biopharmaceutical industry, methods for assessing conformational stability such differential scanning calorimetry and isothermal equilibrium unfolding showed little predictive power and we highlight some of the assumptions and technical challenges of their use with mAbs. Conversely, measures of colloidal stability of the native-state such as preferential interaction coefficients measured by vapor pressure osmometry and solubility assessed by polyethylene-glycol induced precipitation correlated reasonably well with the mAb dimerization data and are most consistent with the excipients tested minimizing dimerization by interacting favorably with the residues comprising the protein-protein association interface.
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Affiliation(s)
- Douglas D Banks
- Department of Biologics Drug Product Development, Celgene Corp, 10300 Campus Point Drive Suite 100, San Diego, California, 92121
| | - Jon F Cordia
- Department of Biologics Drug Product Development, Celgene Corp, 10300 Campus Point Drive Suite 100, San Diego, California, 92121
| | - Vladimir Spasojevic
- Department of Biologics Drug Product Development, Celgene Corp, 10300 Campus Point Drive Suite 100, San Diego, California, 92121
| | - Jeonghoon Sun
- Department of Biotherapeutics, Celgene Corp, 10300 Campus Point Drive Suite 100, San Diego, California, 92121
| | - Sarah Franc
- Department of Biologics Drug Product Development, Celgene Corp, 10300 Campus Point Drive Suite 100, San Diego, California, 92121
| | - Younhee Cho
- Department of Biologics Drug Product Development, Celgene Corp, 10300 Campus Point Drive Suite 100, San Diego, California, 92121
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35
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Oprzeska-Zingrebe EA, Smiatek J. Aqueous Mixtures of Urea and Trimethylamine-N-oxide: Evidence for Kosmotropic or Chaotropic Behavior? J Phys Chem B 2019; 123:4415-4424. [PMID: 31046272 DOI: 10.1021/acs.jpcb.9b02598] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Trimethylamine-N-oxide (TMAO) and urea are commonly produced in many extremophilic microorganisms that live in harsh environments. In view of high temperature, high pressure, or high salt content, TMAO is known as a protein structure stabilizer, whereas urea destabilizes protein structures even under ambient conditions. Despite clear evidence, destabilizers are often regarded as chaotropes, meaning water-structure breakers, whereas kosmotropes as water-structure makers are classified as stabilizers. Using atomistic molecular dynamics simulations, we study aqueous mixtures of TMAO and urea in various biologically relevant concentrations to gain insight into the molecular details of their mutual cross-interactions and their influence on water dynamics and structure. Our results for binary and ternary solutions in combination with different mixing ratios show that both co-solutes strengthen the water network in terms of dynamic and structural aspects. Slight differences in the water binding behavior between both species result in only negligible compensation effects. The outcomes of our simulations thus question the validity and the ill-considered use of attributes like kosmotropic or chaotropic substances for stabilizers and destabilizers.
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Affiliation(s)
| | - Jens Smiatek
- Institute for Computational Physics , University of Stuttgart , D-70569 Stuttgart , Germany.,Helmholtz-Institute Münster: Ionics in Energy Storage (HIMS-IEK 12) , Forschungszentrum Jülich GmbH , D-48149 Münster , Germany
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36
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Levartovsky Y, Shemesh A, Asor R, Raviv U. Effect of Weakly Interacting Cosolutes on Lysozyme Conformations. ACS OMEGA 2018; 3:16246-16252. [PMID: 31458260 PMCID: PMC6643829 DOI: 10.1021/acsomega.8b01289] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 11/15/2018] [Indexed: 06/10/2023]
Abstract
Exposure of a protein to cosolutes, like denaturants, changes its folding equilibrium. To determine the ensemble of protein conformations at equilibrium, in the presence of weakly interacting cosolutes, we present a two-stage analysis of solution X-ray scattering data. In the first stage, Guinier analysis and Kratky plot revealed information about the compactness and flexibility of the protein. In the second stage, elastic network contact model and coarse-grained normal mode analysis were used to generate an ensemble of conformations. The scattering curves of the conformations were computed and fitted to the measured scattering curves to get insights into the dominating folding states at equilibrium. Urea and guanidine hydrochloride (GuHCl) behaved as preferentially included weakly interacting cosolutes and induced denaturation of hen egg-white lysozyme, which served as our test case. The computed models adequately fit the data and gave ensembles of conformations that were consistent with our measurements. The analysis suggests that in the presence of urea, lysozyme retained its compactness and assumed molten globule characteristics, whereas in the presence of GuHCl lysozyme adopted random coiled conformations. Interestingly, no equilibrium intermediate states were observed in both urea and GuHCl.
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37
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Physical Characterization and Stabilization of a Lentiviral Vector Against Adsorption and Freeze-Thaw. J Pharm Sci 2018; 107:2764-2774. [DOI: 10.1016/j.xphs.2018.07.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 06/25/2018] [Accepted: 07/05/2018] [Indexed: 12/13/2022]
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38
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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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39
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Pham QD, Wolde-Kidan A, Gupta A, Schlaich A, Schneck E, Netz RR, Sparr E. Effects of Urea and TMAO on Lipid Self-Assembly under Osmotic Stress Conditions. J Phys Chem B 2018; 122:6471-6482. [DOI: 10.1021/acs.jpcb.8b02159] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Quoc Dat Pham
- Division of Physical Chemistry, Chemistry Department, Lund University, P.O. Box 124, 22100 Lund, Sweden
| | - Amanuel Wolde-Kidan
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Anirudh Gupta
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Alexander Schlaich
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Emanuel Schneck
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Roland R. Netz
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Emma Sparr
- Division of Physical Chemistry, Chemistry Department, Lund University, P.O. Box 124, 22100 Lund, Sweden
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40
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Oprzeska-Zingrebe EA, Smiatek J. Aqueous ionic liquids in comparison with standard co-solutes : Differences and common principles in their interaction with protein and DNA structures. Biophys Rev 2018; 10:809-824. [PMID: 29611033 DOI: 10.1007/s12551-018-0414-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 03/12/2018] [Indexed: 12/29/2022] Open
Abstract
Ionic liquids (ILs) are versatile solvents for a broad range of biotechnological applications. Recent experimental and simulation results highlight the potential benefits of dilute ILs in aqueous solution (aqueous ILs) in order to modify protein and DNA structures systematically. In contrast to a limited number of standard co-solutes like urea, ectoine, trimethylamine-N-oxide (TMAO), or guanidinium chloride, the large amount of possible cation and anion combinations in aqueous ILs can be used to develop tailor-made stabilizers or destabilizers for specific purposes. In this review article, we highlight common principles and differences between aqueous ILs and standard co-solutes with a specific focus on their underlying macromolecular stabilization or destabilization behavior. In combination with statistical thermodynamics theories, we present an efficient framework, which is used to classify structure modification effects consistently. The crucial importance of enthalpic and entropic contributions to the free energy change upon IL-assisted macromolecular unfolding in combination with a complex destabilization mechanism is described in detail. A special focus is also set on aqueous IL-DNA interactions, for which experimental and simulation outcomes are summarized and discussed in the context of previous findings.
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Affiliation(s)
| | - Jens Smiatek
- Institute for Computational Physics, University of Stuttgart, Allmandring 3, 70569, Stuttgart, Germany. .,Helmholtz Institute Münster: Ionics in Energy Storage (HI MS - IEK 12), Forschungszentrum Jülich GmbH, Corrensstrasse 46, 48149, Münster, Germany.
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41
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Roles of osmolytes in protein folding and aggregation in cells and their biotechnological applications. Int J Biol Macromol 2018; 109:483-491. [DOI: 10.1016/j.ijbiomac.2017.12.100] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 12/19/2017] [Indexed: 12/19/2022]
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42
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Diddens D, Lesch V, Heuer A, Smiatek J. Aqueous ionic liquids and their influence on peptide conformations: denaturation and dehydration mechanisms. Phys Chem Chem Phys 2018; 19:20430-20440. [PMID: 28737791 DOI: 10.1039/c7cp02897k] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Low concentrated aqueous ionic liquids (ILs) and their influence on protein structures have attracted a lot of interest over the last few years. This can be mostly attributed to the fact that aqueous ILs, depending on the ion species involved, can be used as protein protectants or protein denaturants. Atomistic molecular dynamics (MD) simulations are performed in order to study the influence of different aprotic ILs on the properties of a short hairpin peptide. Our results reveal distinct binding and denaturation effects for 1-ethyl-3-methylimidazolium (EMIM) in combination with different anions, namely, chloride (CL), tetrafluoroborate (BF4) and acetate (ACE). The simulation outcomes demonstrate that the studied ILs with larger anions reveal a more pronounced accumulation behavior of the individual ion species around the peptide, which is accomplished by a stronger dehydration effect. We can relate these findings to the implications of the Kirkwood-Buff theory, which provides a thermodynamic explanation for the denaturation strength in terms of the IL accumulation behavior. The results for the spatial distribution functions, the binding energies and the local/bulk partition coefficients are in good agreement with metadynamics simulations in order to determine the energetically most stable peptide conformations. The free energy landscapes indicate a decrease of the denaturation strength in the order EMIM/ACE, EMIM/BF4 and EMIM/CL, which coincides with a decreasing size of the anion species. An analysis of the potential binding energies reveals that this effect is mainly of enthalpic nature.
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Affiliation(s)
- Diddo Diddens
- Institute of Physical Chemistry, University of Münster, Corrensstrasse 28/30, 48149 Münster, Germany
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43
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Jamal S, Kumari A, Singh A, Goyal S, Grover A. Conformational Ensembles of α-Synuclein Derived Peptide with Different Osmolytes from Temperature Replica Exchange Sampling. Front Neurosci 2017; 11:684. [PMID: 29270108 PMCID: PMC5725442 DOI: 10.3389/fnins.2017.00684] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 11/22/2017] [Indexed: 11/13/2022] Open
Abstract
Intrinsically disordered proteins (IDP) are a class of proteins that do not have a stable three-dimensional structure and can adopt a range of conformations playing various vital functional role. Alpha-synuclein is one such IDP which can aggregate into toxic protofibrils and has been associated largely with Parkinson's disease (PD) along with other neurodegenerative diseases. Osmolytes are small organic compounds that can alter the environment around the proteins by acting as denaturants or protectants for the proteins. In the present study, we have conducted a series of replica exchange molecular dynamics simulations to explore the role of osmolytes, urea which is a denaturant and TMAO (trimethylamine N-oxide), a protecting osmolyte, in aggregation and conformations of the synuclein peptide. We observed that both the osmolytes have significantly distinct impacts on the peptide and led to transitions of the conformations of the peptide from one state to other. Our findings highlighted that urea attenuated peptide aggregation and resulted in the formation of extended peptide structures whereas TMAO led to compact and folded forms of the peptide.
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Affiliation(s)
- Salma Jamal
- Department of Bioscience and Biotechnology, Banasthali University, Tonk, India
| | - Anchala Kumari
- Department of Biotechnology, TERI School of Advanced Studies, New Delhi, India
| | - Aditi Singh
- Department of Biotechnology, TERI School of Advanced Studies, New Delhi, India
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Sukriti Goyal
- Department of Bioscience and Biotechnology, Banasthali University, Tonk, India
| | - Abhinav Grover
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
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44
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Rabbani G. WITHDRAWN: Role of osmolytes in protein folding and aggregation in cells and its applications in biotechnology. Int J Biol Macromol 2017:S0141-8130(17)32827-1. [PMID: 29137994 DOI: 10.1016/j.ijbiomac.2017.11.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/20/2017] [Accepted: 11/06/2017] [Indexed: 11/26/2022]
Abstract
This article has been withdrawn at the request of the author(s) and/or editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at https://www.elsevier.com/about/our-business/policies/article-withdrawal.
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Affiliation(s)
- Gulam Rabbani
- Department of Medical Biotechnology, YeungNam University, 280 Daehak-ro, Gyeongsan, Gyeongbuk, 38541, Republic of Korea.
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45
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Govrin R, Schlesinger I, Tcherner S, Sivan U. Regulation of Surface Charge by Biological Osmolytes. J Am Chem Soc 2017; 139:15013-15021. [DOI: 10.1021/jacs.7b07036] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Roy Govrin
- Department of Physics and
the Russell Berrie Nanotechnology Institute, Technion−Israel Institute of Technology, Technion City, Haifa 3200003, Israel
| | - Itai Schlesinger
- Department of Physics and
the Russell Berrie Nanotechnology Institute, Technion−Israel Institute of Technology, Technion City, Haifa 3200003, Israel
| | - Shani Tcherner
- Department of Physics and
the Russell Berrie Nanotechnology Institute, Technion−Israel Institute of Technology, Technion City, Haifa 3200003, Israel
| | - Uri Sivan
- Department of Physics and
the Russell Berrie Nanotechnology Institute, Technion−Israel Institute of Technology, Technion City, Haifa 3200003, Israel
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46
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Shimizu S, Smith PE. How Osmolytes Counteract Pressure Denaturation on a Molecular Scale. Chemphyschem 2017; 18:2243-2249. [PMID: 28678423 PMCID: PMC5626881 DOI: 10.1002/cphc.201700503] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 05/30/2017] [Indexed: 11/08/2022]
Abstract
Life in the deep sea exposes enzymes to high hydrostatic pressure, which decreases their stability. For survival, deep sea organisms tend to accumulate various osmolytes, most notably trimethylamine N-oxide used by fish, to counteract pressure denaturation. However, exactly how these osmolytes work remains unclear. Here, a rigorous statistical thermodynamics approach is used to clarify the mechanism of osmoprotection. It is shown that the weak, nonspecific, and dynamic interactions of water and osmolytes with proteins can be characterized only statistically, and that the competition between protein-osmolyte and protein-water interactions is crucial in determining conformational stability. Osmoprotection is driven by a stronger exclusion of osmolytes from the denatured protein than from the native conformation, and water distribution has no significant effect on these changes at low osmolyte concentrations.
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Affiliation(s)
- Seishi Shimizu
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Paul E Smith
- Department of Chemistry, Kansas State University, 213 CBC Building, Manhattan, Kansas, 66506-0401, USA
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47
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Smiatek J. Aqueous ionic liquids and their effects on protein structures: an overview on recent theoretical and experimental results. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:233001. [PMID: 28398214 DOI: 10.1088/1361-648x/aa6c9d] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Ionic liquids (ILs) are used in a variety of technological and biological applications. Recent experimental and simulation results reveal the influence of aqueous ionic liquids on the stability of protein and enzyme structures. Depending on different parameters like the concentration and the ion composition, one can observe distinct stabilization or denaturation mechanisms for various ILs. In this review, we summarize the main findings and discuss the implications with regard to molecular theories of solutions and specific ion effects. A preferential binding model is introduced in order to discuss protein-IL effects from a statistical mechanics perspective. The value of the preferential binding coefficient determines the strength of the ion influence and indicates a shift of the chemical equilibrium either to the native or the denatured state of the protein. We highlight the role of water in order to explain the self-association behavior of the IL species and discuss recent experimental and simulation results in the light of the observed binding effects.
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Affiliation(s)
- Jens Smiatek
- Institute for Computational Physics, University of Stuttgart, Allmandring 3, D-70569 Stuttgart, Germany
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48
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Shimizu S, Stenner R, Matubayasi N. Gastrophysics: Statistical thermodynamics of biomolecular denaturation and gelation from the Kirkwood-Buff theory towards the understanding of tofu. Food Hydrocoll 2017. [DOI: 10.1016/j.foodhyd.2016.07.022] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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49
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Oyetayo OO, Méndez-Lucio O, Bender A, Kiefer H. Diversity selection, screening and quantitative structure–activity relationships of osmolyte-like additive effects on the thermal stability of a monoclonal antibody. Eur J Pharm Sci 2017; 97:151-157. [DOI: 10.1016/j.ejps.2016.11.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 11/11/2016] [Accepted: 11/14/2016] [Indexed: 11/30/2022]
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50
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Sukenik S, Pogorelov TV, Gruebele M. Can Local Probes Go Global? A Joint Experiment-Simulation Analysis of λ(6-85) Folding. J Phys Chem Lett 2016; 7:1960-1965. [PMID: 27101436 DOI: 10.1021/acs.jpclett.6b00582] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The process of protein folding is known to involve global motions in a cooperative affair; the structure of most of the protein sequences is gained or lost over a narrow range of temperature, denaturant, or pressure perturbations. At the same time, recent simulations and experiments reveal a complex structural landscape with a rich set of local motions and conformational changes. We couple experimental kinetic and thermodynamic measurements with specifically tailored analysis of simulation data to isolate local versus global folding probes. We find that local probes exhibit lower melting temperatures, smaller surface area changes, and faster kinetics compared to global ones. We also see that certain local probes of folding match the global behavior more closely than others. Our work highlights the importance of using multiple probes to fully characterize protein folding dynamics by theory and experiment.
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Affiliation(s)
- Shahar Sukenik
- Department of Chemistry, School of Chemical Sciences, and Beckman Institute for Advanced Science and Technology, #National Center for Supercomputing Applications, and ‡Department of Physics and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign , Champaign, Illinois 61801, United States
| | - Taras V Pogorelov
- Department of Chemistry, School of Chemical Sciences, and Beckman Institute for Advanced Science and Technology, #National Center for Supercomputing Applications, and ‡Department of Physics and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign , Champaign, Illinois 61801, United States
| | - Martin Gruebele
- Department of Chemistry, School of Chemical Sciences, and Beckman Institute for Advanced Science and Technology, #National Center for Supercomputing Applications, and ‡Department of Physics and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign , Champaign, Illinois 61801, United States
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