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Ramirez JF, Kumara U, Arulsamy N, Boothby TC. Water content, transition temperature and fragility influence protection and anhydrobiotic capacity. BBA ADVANCES 2024; 5:100115. [PMID: 38318251 PMCID: PMC10840120 DOI: 10.1016/j.bbadva.2024.100115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024] Open
Abstract
Water is essential for metabolism and all life processes. Despite this, many organisms distributed across the kingdoms of life survive near-complete desiccation or anhydrobiosis. Increased intracellular viscosity, leading to the formation of a vitrified state is necessary, but not sufficient, for survival while dry. What properties of a vitrified system make it desiccation-tolerant or -sensitive are unknown. We have analyzed 18 different in vitro vitrified systems, composed of one of three protective disaccharides (trehalose, sucrose, or maltose) and glycerol, quantifying their enzyme-protective capacity and their material properties in a dry state. Protection conferred by mixtures containing maltose correlates strongly with increased water content, increased glass-transition temperature, and reduced glass former fragility, while the protection of glasses formed with sucrose correlates with increased glass transition temperature and the protection conferred by trehalose glasses correlates with reduced glass former fragility. Thus, in vitro different vitrified sugars confer protection through distinct material properties. Next, we examined the material properties of a dry desiccation tolerant and intolerant life stage from three different organisms. The dried desiccation tolerant life stage of all organisms had an increased glass transition temperature and reduced glass former fragility relative to its dried desiccation intolerant life stage. These results suggest in nature organismal desiccation tolerance relies on a combination of various material properties. This study advances our understanding of how protective and non-protective glasses differ in terms of material properties that promote anhydrobiosis. This knowledge presents avenues to develop novel stabilization technologies for pharmaceuticals that currently rely on the cold-chain. Statement of significance For the past three decades the anhydrobiosis field has lived with a paradox, while vitrification is necessary for survival in the dry state, it is not sufficient. Understanding what property(s) distinguishes a desiccation tolerant from an intolerant vitrified system and how anhydrobiotic organisms survive drying is one of the enduring mysteries of organismal physiology. Here we show in vitro the enzyme-protective capacity of different vitrifying sugars can be correlated with distinct material properties. However, in vivo, diverse desiccation tolerant organisms appear to combine these material properties to promote their survival in a dry state.
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Affiliation(s)
- John F. Ramirez
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
| | - U.G.V.S.S. Kumara
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
| | | | - Thomas C. Boothby
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
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Ramirez JF, Kumara U, Arulsamy N, Boothby TC. Water content, transition temperature and fragility influence protection and anhydrobiotic capacity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.30.547256. [PMID: 38014150 PMCID: PMC10680572 DOI: 10.1101/2023.06.30.547256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Water is essential for metabolism and all life processes. Despite this, many organisms distributed across the kingdoms of life survive near-complete desiccation or anhydrobiosis (Greek for "life without water"). Increased intracellular viscosity, leading to the formation of a vitrified state is necessary, but not sufficient, for survival while dry. What properties of a vitrified system make it desiccation-tolerant or -sensitive are unknown. We have analyzed 18 different in vitro vitrified systems, composed of one of three protective disaccharides (trehalose, sucrose, or maltose) and varying amounts of glycerol, quantifying their enzyme-protective capacity and their material properties in a dry state. We find that protection conferred by mixtures containing maltose correlates strongly with increased water content, increased glass-transition temperature, and reduced glass former fragility, while the protection of glasses formed with sucrose correlates with increased glass transition temperature and the protection conferred by trehalose glasses correlates with reduced glass former fragility. Thus, in vitro different vitrified sugars confer protection through distinct material properties. Extending on this, we have examined the material properties of a dry desiccation tolerant and intolerant life stage from three different organisms. In all cases, the dried desiccation tolerant life stage of an organism had an increased glass transition temperature relative to its dried desiccation intolerant life stage, and this trend is also seen in all three organisms when considering reduced glass former fragility. These results suggest that while drying of different protective sugars in vitro results in vitrified systems with distinct material properties that correlate with their enzyme-protective capacity, in nature organismal desiccation tolerance relies on a combination of these properties. This study advances our understanding of how protective and non-protective glasses differ in terms of material properties that promote anhydrobiosis. This knowledge presents avenues to develop novel stabilization technologies for pharmaceuticals that currently rely on the cold-chain.
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Affiliation(s)
- John F. Ramirez
- Department of Molecular Biology, University of Wyoming. Laramie, WY 82071
| | - U.G.V.S.S. Kumara
- Department of Molecular Biology, University of Wyoming. Laramie, WY 82071
| | | | - Thomas C. Boothby
- Department of Molecular Biology, University of Wyoming. Laramie, WY 82071
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Gogovi GK, Silayi S, Shehu A. Computing the Structural Dynamics of RVFV L Protein Domain in Aqueous Glycerol Solutions. Biomolecules 2021; 11:biom11101427. [PMID: 34680060 PMCID: PMC8533350 DOI: 10.3390/biom11101427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/24/2021] [Accepted: 09/25/2021] [Indexed: 11/23/2022] Open
Abstract
Many biological and biotechnological processes are controlled by protein–protein and protein–solvent interactions. In order to understand, predict, and optimize such processes, it is important to understand how solvents affect protein structure during protein–solvent interactions. In this study, all-atom molecular dynamics are used to investigate the structural dynamics and energetic properties of a C-terminal domain of the Rift Valley Fever Virus L protein solvated in glycerol and aqueous glycerol solutions in different concentrations by molecular weight. The Generalized Amber Force Field is modified by including restrained electrostatic potential atomic charges for the glycerol molecules. The peptide is considered in detail by monitoring properties like the root-mean-squared deviation, root-mean-squared fluctuation, radius of gyration, hydrodynamic radius, end-to-end distance, solvent-accessible surface area, intra-potential energy, and solvent–peptide interaction energies for hundreds of nanoseconds. Secondary structure analysis is also performed to examine the extent of conformational drift for the individual helices and sheets. We predict that the peptide helices and sheets are maintained only when the modeling strategy considers the solvent with lower glycerol concentration. We also find that the solvent-peptide becomes more cohesive with decreasing glycerol concentrations. The density and radial distribution function of glycerol solvent calculated when modeled with the modified atomic charges show a very good agreement with experimental results and other simulations at 298.15K.
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Affiliation(s)
- Gideon K. Gogovi
- Department of Mathematics and Statistics, University of Houston—Downtown, Houston, TX 77054, USA
- Correspondence:
| | - Swabir Silayi
- Office of Research Computing, George Mason University, Fairfax, VA 22030, USA;
| | - Amarda Shehu
- Department of Computer Science, George Mason University, Fairfax, VA 22030, USA;
- Department of Bioengineering, George Mason University, Fairfax, VA 22030, USA
- School of Systems Biology, George Mason University, Fairfax, VA 22030, USA
- Center for Advancing Human-Machine Partnerships, George Mason University, Fairfax, VA 22030, USA
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4
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Mutneja A, Karmakar S. Translational dynamics of a rod-like probe in supercooled liquids: an experimentally realizable method to study Stokes-Einstein breakdown, dynamic heterogeneity, and amorphous order. SOFT MATTER 2021; 17:5738-5746. [PMID: 34018543 DOI: 10.1039/d1sm00509j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The use of probe molecules to extract the local dynamical and structural properties of complex dynamical systems is an age-old technique both in simulations and in experiments. A lot of important information which is not immediately accessible from bulk measurements can be accessed via these local measurements. Still, a detailed understanding of how a probe particle dynamics is affected by the surrounding liquid medium is lacking, especially in the supercooled temperature regime. This work shows how the translational dynamics of a rod-like particle immersed in a supercooled liquid can give us information on the growth of the correlation length scales associated with dynamical heterogeneity and the multi-body static correlations in the medium. This work also provides an understanding of the breakdown of Stokes-Einstein and Stokes-Einstein-Debye relations in supercooled liquids along with a unified scaling theory that rationalizes all the observed results. Finally, this work proposes a novel yet simple method accessible in experiments to measure the growth of these important length scales in molecular glass-forming liquids.
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Affiliation(s)
- Anoop Mutneja
- Tata Institute of Fundamental Research, 36/P,Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad, 500107, India.
| | - Smarajit Karmakar
- Tata Institute of Fundamental Research, 36/P,Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad, 500107, India.
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Mukherjee M, Mondal J. Bottom-Up View of the Mechanism of Action of Protein-Stabilizing Osmolytes. J Phys Chem B 2020; 124:11316-11323. [PMID: 33198465 DOI: 10.1021/acs.jpcb.0c06658] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The molecular mechanism of osmolytes on the stabilization of native states of protein is still controversial irrespective of extensive studies over several decades. Recent investigations in terms of experiments and molecular dynamics simulations challenge the popular osmophobic model explaining the mechanistic action of protein-stabilizing osmolytes. The current Perspective presents an updated view on the mechanistic action of osmolytes in light of resurgence of interesting experiments and computer simulations over the past few years in this direction. In this regard, the Perspective adopts a bottom-up approach starting from hydrophobic interactions and eventually adds complexity in the system, going toward the protein, in a complex topology of hydrophobic and electrostatic interactions. Finally, the Perspective unifies osmolyte-induced protein conformational equilibria in terms of preferential interaction theory, irrespective of individual preferential binding or exclusion of osmolytes depending on different osmolytes and protein surfaces. The Perspective also identifies future research directions that can potentially shape this interesting area.
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Affiliation(s)
- Mrinmoy Mukherjee
- Tata Institute of Fundamental Research, Center For Interdisciplinary Sciences, Hyderabad 500107, India
| | - Jagannath Mondal
- Tata Institute of Fundamental Research, Center For Interdisciplinary Sciences, Hyderabad 500107, India
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Mukherjee M, Mondal J, Karmakar S. Role of α and β relaxations in collapsing dynamics of a polymer chain in supercooled glass-forming liquid. J Chem Phys 2019; 150:114503. [PMID: 30901993 DOI: 10.1063/1.5085077] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Understanding the effect of glassy dynamics on the stability of bio-macromolecules and investigating the underlying relaxation processes governing degradation processes of these macromolecules are of immense importance in the context of bio-preservation. In this work, we have studied the stability of a model polymer chain in a supercooled glass-forming liquid at different amounts of supercooling in order to understand how dynamics of supercooled liquids influence the collapse behavior of the polymer. Our systematic computer simulation studies find that, apart from long time relaxation processes (α relaxation), short time dynamics of the supercooled liquid, known as β relaxation, is also correlated with the stability of the model polymer. We also show that anti-plasticizing effect found in this context can be rationalized using the β-relaxation process and how it is modified due to changes in the specific interactions between the biomolecules and the solvent molecules or changes in the local packing around the biomolecules. Our results corroborate with other recent results which suggest that it is important to take in to account both the α and β relaxation times while choosing appropriate bio-preservatives. We believe that our results will have implications in understanding the primary factors in protein stabilization in the context of bio-preservation.
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Affiliation(s)
- Mrinmoy Mukherjee
- Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, 36/P, Gopanpally Village, Serilingampally Mandal, RR District, Hyderabad 500019, India
| | - Jagannath Mondal
- Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, 36/P, Gopanpally Village, Serilingampally Mandal, RR District, Hyderabad 500019, India
| | - Smarajit Karmakar
- Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, 36/P, Gopanpally Village, Serilingampally Mandal, RR District, Hyderabad 500019, India
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7
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Lerbret A, Affouard F. Molecular Packing, Hydrogen Bonding, and Fast Dynamics in Lysozyme/Trehalose/Glycerol and Trehalose/Glycerol Glasses at Low Hydration. J Phys Chem B 2017; 121:9437-9451. [PMID: 28920435 DOI: 10.1021/acs.jpcb.7b07082] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Water and glycerol are well-known to facilitate the structural relaxation of amorphous protein matrices. However, several studies evidenced that they may also limit fast (∼picosecond-nanosecond, ps-ns) and small-amplitude (∼Å) motions of proteins, which govern their stability in freeze-dried sugar mixtures. To determine how they interact with proteins and sugars in glassy matrices and, thereby, modulate their fast dynamics, we performed molecular dynamics (MD) simulations of lysozyme/trehalose/glycerol (LTG) and trehalose/glycerol (TG) mixtures at low glycerol and water concentrations. Upon addition of glycerol and/or water, the glass transition temperature, Tg, of LTG and TG mixtures decreases, the molecular packing of glasses is improved, and the mean-square displacements (MSDs) of lysozyme and trehalose either decrease or increase, depending on the time scale and on the temperature considered. A detailed analysis of the hydrogen bonds (HBs) formed between species reveals that water and glycerol may antiplasticize the fast dynamics of lysozyme and trehalose by increasing the total number and/or the strength of the HBs they form in glassy matrices.
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Affiliation(s)
- Adrien Lerbret
- Univ. Bourgogne Franche-Comté, AgroSup Dijon, UMR A 02.102, PAM, Procédés Alimentaires et Microbiologiques, F-21000 Dijon, France
| | - Frédéric Affouard
- Univ. Lille, CNRS, UMR 8207, UMET, Unité Matériaux Et Transformations, F-59000 Lille, France
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8
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Kalra A, Tishmack P, Lubach JW, Munson EJ, Taylor LS, Byrn SR, Li T. Impact of Supramolecular Aggregation on the Crystallization Kinetics of Organic Compounds from the Supercooled Liquid State. Mol Pharm 2017; 14:2126-2137. [PMID: 28485947 DOI: 10.1021/acs.molpharmaceut.7b00245] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Despite numerous challenges in their theoretical description and practical implementation, amorphous drugs are of growing importance to the pharmaceutical industry. One such challenge is to gain molecular level understanding of the propensity of a molecule to form and remain as a glassy solid. In this study, a series of structurally similar diarylamine compounds was examined to elucidate the role of supramolecular aggregation on crystallization kinetics from supercooled liquid state. The structural similarity of the compounds makes it easier to isolate the molecular features that affect crystallization kinetics and glass forming ability of these compounds. To examine the role of hydrogen-bonded aggregation and motifs on crystallization kinetics, a combination of thermal and spectroscopic techniques was employed. Using variable temperature FTIR, Raman, and solid-state NMR spectroscopies, the presence of hydrogen bonding in the melt and glassy state was examined and correlated with observed phase transition behaviors. Spectroscopic results revealed that the formation of hydrogen-bonded aggregates involving carboxylic acid and pyridine nitrogen (acid-pyridine aggregates) between neighboring molecules in the melt state impedes crystallization, while the presence of carboxylic acid dimers (acid-acid dimers) in the melt favors crystallization. This study suggests that glass formation of small molecules is influenced by the type of intermolecular interactions present in the melt state and the kinetics associated with the molecules to assemble into a crystalline lattice. For the compounds that form acid-pyridine aggregates, the formation of energy degenerate chains, produced due to conformational flexibility of the molecules, presents a kinetic barrier to crystallization. The poor crystallization tendency of these aggregates stems from the highly directional hydrogen-bonding interactions needed to form the acid-pyridine chains. Conversely, for the compounds that form acid-acid dimers, the nondirectional van der Waals forces needed to construct a nucleus promote rapid assembly and crystallization.
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Affiliation(s)
- Arjun Kalra
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University , West Lafayette, Indiana 47907, United States
| | | | - Joseph W Lubach
- Genentech , South San Francisco, California 94080, United States
| | - Eric J Munson
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky 40508, United States
| | - Lynne S Taylor
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University , West Lafayette, Indiana 47907, United States
| | - Stephen R Byrn
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University , West Lafayette, Indiana 47907, United States
| | - Tonglei Li
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University , West Lafayette, Indiana 47907, United States
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9
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Dillon C, Hughes H, O’Reilly NJ, McLoughlin P. Formulation and characterisation of dissolving microneedles for the transdermal delivery of therapeutic peptides. Int J Pharm 2017; 526:125-136. [DOI: 10.1016/j.ijpharm.2017.04.066] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 04/26/2017] [Accepted: 04/27/2017] [Indexed: 12/22/2022]
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10
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Castellanos MM, McAuley A, Curtis JE. Investigating Structure and Dynamics of Proteins in Amorphous Phases Using Neutron Scattering. Comput Struct Biotechnol J 2016; 15:117-130. [PMID: 28138368 PMCID: PMC5257034 DOI: 10.1016/j.csbj.2016.12.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 12/10/2016] [Accepted: 12/13/2016] [Indexed: 02/07/2023] Open
Abstract
In order to increase shelf life and minimize aggregation during storage, many biotherapeutic drugs are formulated and stored as either frozen solutions or lyophilized powders. However, characterizing amorphous solids can be challenging with the commonly available set of biophysical measurements used for proteins in liquid solutions. Therefore, some questions remain regarding the structure of the active pharmaceutical ingredient during freezing and drying of the drug product and the molecular role of excipients. Neutron scattering is a powerful technique to study structure and dynamics of a variety of systems in both solid and liquid phases. Moreover, neutron scattering experiments can generally be correlated with theory and molecular simulations to analyze experimental data. In this article, we focus on the use of neutron techniques to address problems of biotechnological interest. We describe the use of small-angle neutron scattering to study the solution structure of biological molecules and the packing arrangement in amorphous phases, that is, frozen glasses and freeze-dried protein powders. In addition, we discuss the use of neutron spectroscopy to measure the dynamics of glassy systems at different time and length scales. Overall, we expect that the present article will guide and prompt the use of neutron scattering to provide unique insights on many of the outstanding questions in biotechnology.
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Affiliation(s)
- Maria Monica Castellanos
- NIST Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, United States; Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, United States
| | - Arnold McAuley
- Department of Drug Product Development, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320, United States
| | - Joseph E Curtis
- NIST Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, United States
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11
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Indra S, Biswas R. How Heterogeneous Are Trehalose/Glycerol Cryoprotectant Mixtures? A Combined Time-Resolved Fluorescence and Computer Simulation Investigation. J Phys Chem B 2016; 120:11214-11228. [PMID: 27723334 DOI: 10.1021/acs.jpcb.6b06511] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Heterogeneity and molecular motions in representative cryoprotectant mixtures made of trehalose and glycerol are investigated in the temperature range 298 ≤ T (K) ≤ 353, via time-resolved fluorescence Stokes shift and anisotropy measurements, and molecular dynamics simulations of four-point density-time correlations and H-bond relaxations. Mixtures containing 5 and 20 wt % of trehalose along with neat glycerol are studied. Viscosity coefficients for these systems lie in the range 0.30 < η (P) < 23. Measured solute (Coumarin 153) rotation and solvation times reveal a substantial departure from the hydrodynamic viscosity dependence, suggesting the strong microheterogeneous nature of these systems. Fluorescence anisotropy decays are highly nonexponential, reflecting a non-Markovian character of the medium friction. A complete missing of the Stokes shift dynamics in these systems at 298 K but partial detection of it at other higher temperatures (shift magnitude being ∼400-600 cm-1) indicates rigid solute environments. An amorphous solid-like feature emerges in the simulated radial distribution functions at these temperatures. Analyses of mean squared displacements reveal rattling-in-a-cage motion, non-Gaussian displacement distributions, and strong dynamic heterogeneity features. Simulated dynamic structure factors and four-point correlations hint, respectively, at very long α-relaxation and correlated time scales at 298 K. This explains the long solute rotation times (∼80-200 ns) measured at 298 K. Stretched exponential decay of the simulated H-bond relaxations with long time scales further highlights the strong temporal heterogeneity and slow dynamics inherent to these systems. In summary, this work provides the first insight into the molecular motions and interspecies interaction in a representative cryoprotectant mixture, and stimulates further study to investigate the interconnection between cryoprotection and dynamic heterogeneity.
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Affiliation(s)
- Sandipa Indra
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences , Block-JD, Salt Lake, Sector-III, Kolkata 700106, India
| | - Ranjit Biswas
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences , Block-JD, Salt Lake, Sector-III, Kolkata 700106, India
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12
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Ubbink J. Structural and thermodynamic aspects of plasticization and antiplasticization in glassy encapsulation and biostabilization matrices. Adv Drug Deliv Rev 2016; 100:10-26. [PMID: 26748258 DOI: 10.1016/j.addr.2015.12.019] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 12/22/2015] [Accepted: 12/23/2015] [Indexed: 01/21/2023]
Abstract
The structural and thermodynamic properties of glassy carbohydrate matrices for the encapsulation and biostabilization of sensitive bioactive compounds, such as pharmaceutically active proteins and oxidation-sensitive compounds, are reviewed in the context of the plasticization and antiplasticization of glassy carbohydrates of intermediate and high molecular weight by low molecular weight diluents. Plasticization and antiplasticization may be monitored either by dynamic measures or by structural and thermodynamic features of the glassy matrices. Specifically, it is demonstrated that the decrease in size of the molecular free volume holes with increasing diluent content, as determined by positron annihilation lifetime spectroscopy (PALS), is related to the antiplasticization of glassy carbohydrate matrices, resulting in increased barrier properties of the glassy matrix. As far as could be ascertained from the available data, the regimes as identified by PALS map on those detected by neutron scattering and dielectric spectroscopy for glassy matrices consisting of trehalose and the diluent glycerol. The review is concluded by a survey of the published results on the stability of bioactive compounds encapsulated in carbohydrate glasses and an overview of outstanding questions.
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13
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Towey JJ, Soper AK, Dougan L. Low-Density Water Structure Observed in a Nanosegregated Cryoprotectant Solution at Low Temperatures from 285 to 238 K. J Phys Chem B 2016; 120:4439-48. [DOI: 10.1021/acs.jpcb.6b01185] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- J. J. Towey
- Faculty
of Engineering, University of Nottingham, Nottingham NG7 2NR, U.K
| | - A. K. Soper
- ISIS
Facility, Rutherford Appleton Laboratory, Chilton, Didcot, Oxon OX11 OQX, U.K
| | - L. Dougan
- School
of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, U.K
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14
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Khodadadi S, Sokolov AP. Protein dynamics: from rattling in a cage to structural relaxation. SOFT MATTER 2015; 11:4984-4998. [PMID: 26027652 DOI: 10.1039/c5sm00636h] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We present an overview of protein dynamics based mostly on results of neutron scattering, dielectric relaxation spectroscopy and molecular dynamics simulations. We identify several major classes of protein motions on the time scale from faster than picoseconds to several microseconds, and discuss the coupling of these processes to solvent dynamics. Our analysis suggests that the microsecond backbone relaxation process might be the main structural relaxation of the protein that defines its glass transition temperature, while faster processes present some localized secondary relaxations. Based on the overview, we formulate a general picture of protein dynamics and discuss the challenges in this field.
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Affiliation(s)
- S Khodadadi
- Faculty of Applied Sciences, Delft University of Technology, Delft, The Netherlands
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15
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Weng L, Elliott GD. Local minimum in fragility for trehalose/glycerol mixtures: implications for biopharmaceutical stabilization. J Phys Chem B 2015; 119:6820-7. [PMID: 25955786 DOI: 10.1021/acs.jpcb.5b01675] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Approximately a decade ago it was observed that adding a small amount (5 wt %) of glycerol to trehalose could substantially improve the stability of enzymes stored in these glasses even though the final glass transition temperature (Tg) was reduced by ∼20 K. This finding inspired great interest in the fast dynamics of dehydrated trehalose/glycerol mixtures, leading to the observation that suppression of fast dynamics was optimal in the presence of ∼5 wt % of glycerol. It was also recognized that the fast dynamics should, in theory, be related to the fragility of these glass formers, but experimental confirmation of this hypothesis has been lacking for trehalose/glycerol mixtures or any other mixtures of this nature. In the present study a dynamic mechanical analyzer (DMA) was used to determine both the Tg and the kinetic fragility index (m) of trehalose/glycerol mixtures within the mass fraction range of 80-100 wt % of trehalose. It was found that the fragility index correlated with the mass fraction of trehalose in a nonmonotonic manner, with a local minimum between 87.5 and 95 wt % of trehalose, whereas the composition dependence of Tg was found to follow a Gordon-Taylor-like relationship, with no local minimum. The composition of 5-12.5 wt % glycerol in trehalose thus yielded a matrix that maximized the strong glass-forming contribution of glycerol, while minimizing its Tg lowering effect. This quantitative evidence supports speculation about the fragility characteristics of these mixtures that has been ongoing for the past decade. The DMA-based Tg and fragility determination method developed in this study represents a new approach for identifying optimal compositions for preservation of biologics.
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Affiliation(s)
- Lindong Weng
- Department of Mechanical Engineering and Engineering Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Gloria D Elliott
- Department of Mechanical Engineering and Engineering Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
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16
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Weng L, Elliott GD. Determination of the relaxation characteristics of sugar glasses embedded in microfiber substrates. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2014; 44:422-9. [PMID: 25280724 DOI: 10.1016/j.msec.2014.08.048] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 07/17/2014] [Accepted: 08/24/2014] [Indexed: 11/18/2022]
Abstract
Recently there has been considerable interest in developing sugar glasses that enable storage of biologics without refrigeration. Microfiber filter papers are good substrates for drying biologics in the presence of sugar glass-formers, providing for an even distribution of samples and an enhanced surface area for drying, but the opaqueness prevents macroscopic observation of the sample and can introduce complexities that impede physical characterization. Because drying kinetics and processing conditions can impact the relaxation dynamics (e.g., α- and β-relaxation), which can influence the efficacy of the glass as a stabilizer, methods are needed that can enable a determination of relaxation phenomena of sugar glasses in such complex environments. In this study we present a method which provides verification of the absence of crystallinity following drying on glass fiber filter paper and also enables the determination of relaxation characteristics of amorphous sugar compositions embedded within these filter substrates. Using material pockets to contain the sugar glass-embedded microfiber paper, the α-relaxation temperature, Tα, was determined as a function of the water content in trehalose and sucrose samples using Dynamic Mechanical Analysis (DMA). Results were verified by comparison with previous calorimetric and spectroscopic studies. The data also demonstrated the plasticizing effects of water, as Tα was shown to correlate with water content via a Gordon-Taylor-like relationship. Our findings validate a new approach for determining the relaxation characteristics of microfiber embedded sugar glasses, and offer new insights into the relaxation characteristics of glasses prepared by microwave-assisted drying on filter papers.
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Affiliation(s)
- Lindong Weng
- Department of Mechanical Engineering and Engineering Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, United States
| | - Gloria D Elliott
- Department of Mechanical Engineering and Engineering Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, United States.
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17
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Quddus MAAR, Rojas OJ, Pasquinelli MA. Molecular dynamics simulations of the adhesion of a thin annealed film of oleic acid onto crystalline cellulose. Biomacromolecules 2014; 15:1476-83. [PMID: 24650049 DOI: 10.1021/bm500088c] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular dynamics simulations were used to characterize the wetting behavior of crystalline cellulose planes in contact with a thin oily film of oleic acid. Cellulose crystal planes with higher molecular protrusions and increased surface area produced stronger adhesion if compared to other crystal planes due to enhanced wetting and hydrogen bonding. The detailed characteristics of crystal plane features and the contribution of directional hydrogen bonding was investigated. Similarly, oleophilicity of the cellulose planes increased with the increase in surface roughness and number of directional hydrogen bonds. These results correlate with conclusions drawn from experimental studies such as adhesion of an ink vehicle on cellulose surface.
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Affiliation(s)
- Mir A A R Quddus
- Fiber and Polymer Science Program and §Forest Biomaterials, North Carolina State University , Raleigh, North Carolina 27695, United States
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18
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He X, Lopes PEM, MacKerell AD. Polarizable empirical force field for acyclic polyalcohols based on the classical Drude oscillator. Biopolymers 2013; 99:724-38. [PMID: 23703219 PMCID: PMC3902549 DOI: 10.1002/bip.22286] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 05/05/2013] [Indexed: 01/12/2023]
Abstract
A polarizable empirical force field for acyclic polyalcohols based on the classical Drude oscillator is presented. The model is optimized with an emphasis on the transferability of the developed parameters among molecules of different sizes in this series and on the condensed-phase properties validated against experimental data. The importance of the explicit treatment of electronic polarizability in empirical force fields is demonstrated in the cases of this series of molecules with vicinal hydroxyl groups that can form cooperative intra- and intermolecular hydrogen bonds. Compared to the CHARMM additive force field, improved treatment of the electrostatic interactions avoids overestimation of the gas-phase dipole moments resulting in significant improvement in the treatment of the conformational energies and leads to the correct balance of intra- and intermolecular hydrogen bonding of glycerol as evidenced by calculated heat of vaporization being in excellent agreement with experiment. Computed condensed phase data, including crystal lattice parameters and volumes and densities of aqueous solutions are in better agreement with experimental data as compared to the corresponding additive model. Such improvements are anticipated to significantly improve the treatment of polymers in general, including biological macromolecules.
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Affiliation(s)
- Xibing He
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201
| | - Pedro E. M. Lopes
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201
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Corradini D, Strekalova EG, Stanley HE, Gallo P. Microscopic mechanism of protein cryopreservation in an aqueous solution with trehalose. Sci Rep 2013; 3:1218. [PMID: 23390573 PMCID: PMC3565168 DOI: 10.1038/srep01218] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Accepted: 01/22/2013] [Indexed: 01/15/2023] Open
Abstract
In order to investigate the cryoprotective mechanism of trehalose on proteins, we use molecular dynamics computer simulations to study the microscopic dynamics of water upon cooling in an aqueous solution of lysozyme and trehalose. We find that the presence of trehalose causes global retardation of the dynamics of water. Comparing aqueous solutions of lysozyme with/without trehalose, we observe that the dynamics of water in the hydration layers close to the protein is dramatically slower when trehalose is present in the system. We also analyze the structure of water and trehalose around the lysozyme and find that the trehalose molecules form a cage surrounding the protein that contains very slow water molecules. We conclude that the transient cage of trehalose molecules that entraps and slows the water molecules prevents the crystallisation of protein hydration water upon cooling.
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Affiliation(s)
- Dario Corradini
- Center for Polymer Studies and Department of Physics, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, USA.
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20
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Magazù S, Migliardo F, Gonzalez MA, Mondelli C, Parker SF, Vertessy BG. Molecular mechanisms of survival strategies in extreme conditions. Life (Basel) 2012; 2:364-76. [PMID: 25371270 PMCID: PMC4187154 DOI: 10.3390/life2040364] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 11/08/2012] [Accepted: 11/26/2012] [Indexed: 01/04/2023] Open
Abstract
Today, one of the major challenges in biophysics is to disclose the molecular mechanisms underlying biological processes. In such a frame, the understanding of the survival strategies in extreme conditions received a lot of attention both from the scientific and applicative points of view. Since nature provides precious suggestions to be applied for improving the quality of life, extremophiles are considered as useful model-systems. The main goal of this review is to present an overview of some systems, with a particular emphasis on trehalose playing a key role in several extremophile organisms. The attention is focused on the relation among the structural and dynamic properties of biomolecules and bioprotective mechanisms, as investigated by complementary spectroscopic techniques at low- and high-temperature values.
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Affiliation(s)
- Salvatore Magazù
- Department of Physics, University of Messina, Viale D'Alcontres 31, P.O. Box 55-98166, Messina, Italy.
| | - Federica Migliardo
- Department of Physics, University of Messina, Viale D'Alcontres 31, P.O. Box 55-98166, Messina, Italy.
| | - Miguel A Gonzalez
- Institut Laue Langevin, 6, Rue Jules Horowitz, F-38042 Grenoble Cedex 9, France.
| | - Claudia Mondelli
- CNR-IOM-OGG, Institut Laue Langevin, 6, Rue Jules Horowitz, F-38042 Grenoble Cedex 9, France.
| | - Stewart F Parker
- ISIS Facility, Rutherford Appleton Laboratory, Chilton, Oxon, OX11 0QX, UK.
| | - Beata G Vertessy
- Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Science, Budapest, Hungary.
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Lerbret A, Affouard F, Hédoux A, Krenzlin S, Siepmann J, Bellissent-Funel MC, Descamps M. How strongly does trehalose interact with lysozyme in the solid state? Insights from molecular dynamics simulation and inelastic neutron scattering. J Phys Chem B 2012; 116:11103-16. [PMID: 22894179 DOI: 10.1021/jp3058096] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Therapeutic proteins are usually conserved in glassy matrixes composed of stabilizing excipients and a small amount of water, which both control their long-term stability, and thus their potential use in medical treatments. To shed some light on the protein-matrix interactions in such systems, we performed molecular dynamics (MD) simulations on matrixes of (i) the model globular protein lysozyme (L), (ii) the well-known bioprotectant trehalose (T), and (iii) the 1:1 (in weight) lysozyme/trehalose mixture (LT), at hydration levels h of 0.0, 0.075, and 0.15 (in g of water/g of protein or sugar). We also supplemented these simulations with complementary inelastic neutron scattering (INS) experiments on the L, T, and LT lyophilized (freeze-dried) samples. The densities and free volume distributions indicate that trehalose improves the molecular packing of the LT glass with respect to the L one. Accordingly, the low-frequency vibrational densities of states (VDOS) and the mean square displacements (MSDs) of lysozyme reveal that it is less flexible-and thus less likely to unfold-in the presence of trehalose. Furthermore, at low contents (h = 0.075), water systematically stiffens the vibrational motions of lysozyme and trehalose, whereas it increases their MSDs on the nanosecond (ns) time scale. This stems from the hydrogen bonds (HBs) that lysozyme and trehalose form with water, which, interestingly, are stronger than the ones they form with each other but which, nonetheless, relax faster on the ns time scale, given the larger mobility of water. Moreover, lysozyme interacts preferentially with water in the hydrated LT mixtures, and trehalose appears to slow down significantly the relaxation of lysozyme-water HBs. Overall, our results suggest that the stabilizing efficiency of trehalose arises from its ability to (i) increase the number of HBs formed by proteins in the dry state and (ii) make the HBs formed by water with proteins stable on long (>ns) time scales.
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Affiliation(s)
- Adrien Lerbret
- Unité Matériaux Et Transformations, UMR CNRS 8207, Université Lille Nord de France, USTL, 59655 Villeneuve d'Ascq, France.
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Magazù S, Migliardo F, Affouard F, Descamps M, Telling MTF. Study of the relaxational and vibrational dynamics of bioprotectant glass-forming mixtures by neutron scattering and molecular dynamics simulation. J Chem Phys 2010. [DOI: 10.1063/1.3407428] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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24
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Anarchy in the solid state: structural dependence on glass-forming ability in triazine-based molecular glasses. Tetrahedron 2009. [DOI: 10.1016/j.tet.2009.07.026] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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25
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Jain P, Sen S, Risbud SH. Effect of glass-forming biopreservatives on head group rotational dynamics in freeze-dried phospholipid bilayers: A P31 NMR study. J Chem Phys 2009; 131:025102. [DOI: 10.1063/1.3170927] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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26
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Busselez R, Lefort R, Guendouz M, Frick B, Merdrignac-Conanec O, Morineau D. Molecular dynamics of glycerol and glycerol-trehalose bioprotectant solutions nanoconfined in porous silicon. J Chem Phys 2009; 130:214502. [DOI: 10.1063/1.3147222] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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27
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Tang CH, Su LY, Tseng WC. Using trehalose delivered by the intramuscular injection of plasmid DNA as an adjuvant for transgene expression. J Gene Med 2009; 11:250-6. [PMID: 19152373 DOI: 10.1002/jgm.1295] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND Intramuscular injection is a popular and effective approach to administer naked plasmid for transgene expression. The use of an adjuvant can provide a straightforward approach for enhancing transgene expression. METHODS Expression plasmid was formulated with various concentrations of trehalose for injection into the skeletal muscles of C57BL/6 mice. The effects of trehalose on gene dosage and the duration of transgene expression were assessed. The levels of transgene expression were indicated by levels of luciferase expression of the homogenized whole skeletal muscle or by histological X-gal staining of beta-galactosidase expression. Trehalose was also added to serum to examine the ability of protecting the DNA from degradation. RESULTS It was found that an optimal trehalose concentration of 10 mM will achieve a level of transgene expression that is seven-fold higher than in the absence of trehalose. When compared with other disaccharides, only the incorporation of trehalose can effectively enhance transgene expression. Trehalose is able to improve transgene expression by intramuscular injection at a low gene dosage as well as prolong the duration of transgene expression. CONCLUSIONS Trehalose is an effective adjuvant for intramuscular administration of naked plasmid with respect to both enhanced levels and prolonged duration of transgene expression, most likely due to retarding plasmid degradation.
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Affiliation(s)
- Chien-Hsiang Tang
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei, Taiwan
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28
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Elmoazzen HY, Lee GY, Li MW, McGinnis LK, Lloyd KCK, Toner M, Biggers JD. Further optimization of mouse spermatozoa evaporative drying techniques. Cryobiology 2009; 59:113-5. [PMID: 19375415 DOI: 10.1016/j.cryobiol.2009.03.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2009] [Revised: 03/24/2009] [Accepted: 03/27/2009] [Indexed: 11/26/2022]
Abstract
It has been shown in the past that mouse spermatozoa could be dried under a stream of nitrogen gas at ambient temperature and stored at 4 degrees C or 22 degrees C for up to 3 months and was capable of generating live-born offspring. In previous desiccation work, dried sperm were stored in a vacuum-sealed plastic bag placed in a vacuum-packed Mylar bag. However, dried specimens stored in this way often lost moisture, particularly in samples stored at higher temperatures (22 degrees C) compared to lower temperatures (4 degrees C). The present report describes a method which minimizes this water loss from the dried sperm samples. Its use is described in a preliminary study on the effect of supplementing the trehalose with glycerol. The results have demonstrated that mouse sperm can be stored at 4 degrees C over saturated NaBr without the uptake of water which occurs when they are stored in Mylar packages. In addition, we were able to get some survival of sperm (9-15%) at room temperature storage after 3 months. The addition of glycerol to trehalose had little effect on the survival of dried mouse sperm stored over NaBr for 1 and 3 months.
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Affiliation(s)
- Heidi Y Elmoazzen
- Center for Engineering in Medicine, Massachusetts General Hospital, Harvard Medical School and Shriners Hospital for Children, Boston, MA 02115, USA.
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Malsam J, Aksan A. Hydrogen Bonding and Kinetic/Thermodynamic Transitions of Aqueous Trehalose Solutions at Cryogenic Temperatures. J Phys Chem B 2009; 113:6792-9. [DOI: 10.1021/jp8099434] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jason Malsam
- Biostabilization Laboratory, Department of Mechanical Engineering, University of Minnesota, Minneapolis, Minnesota 55455
| | - Alptekin Aksan
- Biostabilization Laboratory, Department of Mechanical Engineering, University of Minnesota, Minneapolis, Minnesota 55455
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30
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Wang R, Pellerin C, Lebel O. Role of hydrogen bonding in the formation of glasses by small molecules: a triazine case study. ACTA ACUST UNITED AC 2009. [DOI: 10.1039/b820294j] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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31
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Psurek T, Soles CL, Page KA, Cicerone MT, Douglas JF. Quantifying Changes in the High-Frequency Dynamics of Mixtures by Dielectric Spectroscopy. J Phys Chem B 2008; 112:15980-90. [DOI: 10.1021/jp8034314] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tatiana Psurek
- Polymers Division, National Institute of Standards and Technology, Gaithersburg, MD 20899
| | - Christopher L. Soles
- Polymers Division, National Institute of Standards and Technology, Gaithersburg, MD 20899
| | - Kirt A. Page
- Polymers Division, National Institute of Standards and Technology, Gaithersburg, MD 20899
| | - Marcus T. Cicerone
- Polymers Division, National Institute of Standards and Technology, Gaithersburg, MD 20899
| | - Jack F. Douglas
- Polymers Division, National Institute of Standards and Technology, Gaithersburg, MD 20899
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32
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Riggleman RA, de Pablo JJ. Antiplasticization and local elastic constants in trehalose and glycerol mixtures. J Chem Phys 2008; 128:224504. [DOI: 10.1063/1.2925684] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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33
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Lerbret A, Affouard F, Bordat P, Hédoux A, Guinet Y, Descamps M. Molecular dynamics simulations of lysozyme in water/sugar solutions. Chem Phys 2008. [DOI: 10.1016/j.chemphys.2007.09.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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34
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Yongye AB, Foley BL, Woods RJ. On achieving experimental accuracy from molecular dynamics simulations of flexible molecules: aqueous glycerol. J Phys Chem A 2008; 112:2634-9. [PMID: 18311953 PMCID: PMC4201037 DOI: 10.1021/jp710544s] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The rotational isomeric states (RIS) of glycerol at infinite dilution have been characterized in the aqueous phase via a 1 micros conventional molecular dynamics (MD) simulation, a 40 ns enhanced sampling replica exchange molecular dynamics (REMD) simulation, and a reevaluation of the experimental NMR data. The MD and REMD simulations employed the GLYCAM06/AMBER force field with explicit treatment of solvation. The shorter time scale of the REMD sampling method gave rise to RIS and theoretical scalar 3J(HH) coupling constants that were comparable to those from the much longer traditional MD simulation. The 3J(HH) coupling constants computed from the MD methods were in excellent agreement with those observed experimentally. Despite the agreement between the computed and the experimental J-values, there were variations between the rotamer populations computed directly from the MD data and those derived from the experimental NMR data. The experimentally derived populations were determined utilizing limiting J-values from an analysis of NMR data from substituted ethane molecules and may not be completely appropriate for application in more complex molecules, such as glycerol. Here, new limiting J-values have been derived via a combined MD and quantum mechanical approach and were used to decompose the experimental 3J(HH) coupling constants into population distributions for the glycerol RIS.
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Affiliation(s)
- Austin B. Yongye
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, Georgia 30602
| | - B. Lachele Foley
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, Georgia 30602
| | - Robert J. Woods
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, Georgia 30602
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Abstract
The dynamics of a folded protein is studied in water and glycerol at a series of temperatures below and above their respective dynamical transition. The system is modeled in two distinct states whereby the protein is decoupled from the bulk solvent at low temperatures, and communicates with it through a vicinal layer at physiological temperatures. A linear viscoelastic model elucidates the less-than-expected increase in the relaxation times observed in the backbone dynamics of the protein. The model further explains the increase in the flexibility of the protein once the transition takes place and the differences in the flexibility under the different solvent environments. Coupling between the vicinal layer and the protein fluctuations is necessary to interpret these observations. The vicinal layer is postulated to form once a threshold for the volumetric fluctuations in the protein to accommodate solvents of different sizes is reached. Compensation of entropic-energetic contributions from the protein-coupled vicinal layer quantifies the scaling of the dynamical transition temperatures in various solvents. The protein adapts different conformational routes for organizing the required coupling to a specific solvent, which is achieved by adjusting the amount of conformational jumps in the surface-group dihedrals.
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Affiliation(s)
- Canan Atilgan
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey.
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36
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Wu C, Xu W. Atomistic simulation study of absorbed water influence on structure and properties of crosslinked epoxy resin. POLYMER 2007. [DOI: 10.1016/j.polymer.2007.06.038] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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37
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Dirama TE, Curtis JE, Carri GA, Sokolov AP. Coupling between lysozyme and trehalose dynamics: microscopic insights from molecular-dynamics simulations. J Chem Phys 2007; 124:034901. [PMID: 16438608 DOI: 10.1063/1.2159471] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We have carried out molecular-dynamics simulations on fully flexible all-atom models of the protein lysozyme immersed in trehalose, an effective biopreservative, with the purpose of exploring the nature and extent of the dynamical coupling between them. Our study shows a strong coupling over a wide range of temperatures. We found that the onset of anharmonic behavior was dictated by changes in the dynamics and relaxation processes in the trehalose glass. The physical origin of protein-trehalose coupling was traced to the hydrogen bonds formed at the interface between the protein and the solvent. Moreover, protein-solvent hydrogen bonding was found to control the structural relaxation of the protein. The dynamics of the protein was found to be heterogeneous; the motions of surface and core atoms had different dependencies on temperature and, in addition, the surface atoms were more sensitive to the dynamics of the solvent than the core atoms. From the solvent perspective we found that the dynamics near the protein surface showed an unexpected enhanced mobility compared to the bulk. These results shed some light on the microscopic origins of the dynamical coupling in protein-solvent systems.
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Affiliation(s)
- Taner E Dirama
- Department of Polymer Science, The University of Akron, Akron, Ohio 44325-3909, USA
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38
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Lefort R, Bordat P, Cesaro A, Descamps M. Exploring the conformational energy landscape of glassy disaccharides by cross polarization magic angle spinning C13 nuclear magnetic resonance and numerical simulations. II. Enhanced molecular flexibility in amorphous trehalose. J Chem Phys 2007; 126:014511. [PMID: 17212504 DOI: 10.1063/1.2409935] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
This paper uses chemical shift surfaces to simulate experimental (13)C cross polarization magic angle spinning spectra for amorphous solid state disaccharides, paying particular attention to the glycosidic linkage atoms in trehalose, sucrose, and lactose. The combination of molecular mechanics with density functional theory/gauge invariant atomic orbital ab initio methods provides reliable structural information on the conformational distribution in the glass. The results are interpreted in terms of an enhanced flexibility that trehalose possesses in the amorphous solid state, at least on the time scale of (13)C nuclear magnetic resonance measurements. Implications of these findings for the fragility of trehalose glass and bioprotectant action are discussed.
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Affiliation(s)
- Ronan Lefort
- Groupe Matière Condensée et Matériaux, Unversité de Rennes 1, Campus de Beaulieu, F-35042 Rennes Cedex, France
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39
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Modelling the interaction of several bisphosphonates with hydroxyapatite using the generalised AMBER force field. J Mol Struct 2006. [DOI: 10.1016/j.molstruc.2006.04.032] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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40
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Curtis JE, Dirama TE, Carri GA, Tobias DJ. Inertial Suppression of Protein Dynamics in a Binary Glycerol−Trehalose Glass. J Phys Chem B 2006; 110:22953-6. [PMID: 17107124 DOI: 10.1021/jp0615499] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The traditional approach used to predict the ability of a glassy matrix to maximally preserve the activity of a protein solute is the glass transition temperature (T(g)) of the glass. Recently it has been shown that the addition of a low T(g) diluent (glycerol) can rigidify the structure of a high T(g) glassy matrix in binary glycerol-trehalose glasses. The optimal density of glycerol in trehalose minimizes the average mean square displacements of non-exchangeable protons in the glass samples. The amount of glycerol added to a trehalose glass coincides with the maximal recovery of biological activity in a separate study using similar binary glass samples. In this study, we use molecular dynamics (MD) simulations to investigate the dynamics of a hydrated protein encased in glycerol, unary trehalose and binary glycerol-trehalose glasses. We have found that we are able to reproduce the rigidification of the glycerol-trehalose glassy matrix and that there is a direct correlation between bulk glass dynamics and the extent of atomic fluctuation of protein atoms. The detailed microscopic picture that emerges is that protein dynamics are suppressed mainly by inertia of the bulk glass and to a lesser extent specific interactions at the protein-solvent interface. Thus, the inertia of the glassy matrix may be an influential factor in the determination of pharmaceutically relevant formulations.
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41
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Lebel O, Maris T, Perron ME, Demers E, Wuest JD. The Dark Side of Crystal Engineering: Creating Glasses from Small Symmetric Molecules that Form Multiple Hydrogen Bonds. J Am Chem Soc 2006; 128:10372-3. [PMID: 16895395 DOI: 10.1021/ja063353s] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Glasses made from compounds of low molecular weight are useful materials with many attractive features, including well-defined compositions. At present, there are no reliable ways to identify molecules that will form long-lived glasses, and efforts to design them have tended to rely on crude principles, such as avoiding small, symmetric, and relatively inflexible molecules that engage in strong intermolecular association. We have found that it is possible to make glasses from such molecules by turning to the dark side of crystal engineering and by making small but carefully selected structural modifications specifically designed to thwart established patterns of crystallization.
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Affiliation(s)
- Olivier Lebel
- Département de Chimie, Université de Montréal, Montréal, Québec H3C 3J7, Canada
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Dirama TE, Carri GA, Sokolov AP. Coupling between lysozyme and glycerol dynamics: Microscopic insights from molecular-dynamics simulations. J Chem Phys 2005; 122:244910. [PMID: 16035819 DOI: 10.1063/1.1938191] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We explore possible molecular mechanisms behind the coupling of protein and solvent dynamics using atomistic molecular-dynamics simulations. For this purpose, we analyze the model protein lysozyme in glycerol, a well-known protein-preserving agent. We find that the dynamics of the hydrogen bond network between the solvent molecules in the first shell and the surface residues of the protein controls the structural relaxation (dynamics) of the whole protein. Specifically, we find a power-law relationship between the relaxation time of the aforementioned hydrogen bond network and the structural relaxation time of the protein obtained from the incoherent intermediate scattering function. We demonstrate that the relationship between the dynamics of the hydrogen bonds and the dynamics of the protein appears also in the dynamic transition temperature of the protein. A study of the dynamics of glycerol as a function of the distance from the surface of the protein indicates that the viscosity seen by the protein is not the one of the bulk solvent. The presence of the protein suppresses the dynamics of the surrounding solvent. This implies that the protein sees an effective viscosity higher than the one of the bulk solvent. We also found significant differences in the dynamics of surface and core residues of the protein. The former is found to follow the dynamics of the solvent more closely than the latter. These results allowed us to propose a molecular mechanism for the coupling of the solvent-protein dynamics.
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Affiliation(s)
- Taner E Dirama
- Department of Polymer Science, The University of Akron, Ohio 44325, USA
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