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Gomes I, Martins GF, Galamba N. Essential dynamics of ubiquitin in water and in a natural deep eutectic solvent. Phys Chem Chem Phys 2024; 26:18244-18255. [PMID: 38904333 DOI: 10.1039/d4cp01773k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Natural deep eutectic solvents (NADESs) comprised of osmolytes are of interest as potential biomolecular (cryo)protectants. However, the way these solvents influence the structure and dynamics of biomolecules as well as the role of water remains poorly understood. We carried out principal component analysis of various secondary structure elements of ubiquitin in water and a betaine : glycerol : water (1 : 2 : ζ; ζ = 0, 1, 2, 5, 10, 20, 45) NADES, from molecular dynamics trajectories, to gain insight into the protein dynamics as it undergoes a transition from a highly viscous anhydrous to an aqueous environment. A crossover of the protein's essential dynamics at ζ ∼ 5, induced by solvent-shell coupled fluctuations, is observed, indicating that ubiquitin might (re)fold in the NADES upon water addition at ζ > ∼5. Further, in contrast to water, the anhydrous NADES preserves ubiquitin's essential modes at high temperatures explaining the protein's seemingly enhanced thermal stability.
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Affiliation(s)
- Inês Gomes
- BioISI - Biosystems and Integrative Sciences Institute, Faculty of Sciences of the University of Lisbon, C8, Campo Grande, 1749-016 Lisbon, Portugal.
| | - Gabriel F Martins
- BioISI - Biosystems and Integrative Sciences Institute, Faculty of Sciences of the University of Lisbon, C8, Campo Grande, 1749-016 Lisbon, Portugal.
| | - Nuno Galamba
- BioISI - Biosystems and Integrative Sciences Institute, Faculty of Sciences of the University of Lisbon, C8, Campo Grande, 1749-016 Lisbon, Portugal.
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2
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Gomes I, Galamba N. Protein stability in a natural deep eutectic solvent: Preferential hydration or solvent slaving? J Chem Phys 2023; 159:235101. [PMID: 38099555 DOI: 10.1063/5.0177095] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
Deep eutectic solvents (DESs) emerged as potential alternative solvent media in multiple areas, including biomolecular (cryo)preservation. Herein, we studied the stability of a small protein (ubiquitin) in water and a betaine-glycerol-water (B:G:W) (1:2:ζ; ζ = 0, 1, 2, 5, 10) DES, through molecular dynamics. An AMBER-based model that accurately describes the density and shear viscosity of the DES is proposed. We find that water molecules are largely trapped in the solvent, precluding the formation of a full hydration layer, seemingly opposite to osmolytes' preferential exclusion/preferential hydration mechanism. Although the protein is stable in the DES, structural fluctuations are largely suppressed and only recovered upon sufficient hydration. This is explained by a solvent-slaving mechanism where β-fluctuations are key, with the non-monotonic hydration of some amino acids with the water content providing an explanation to the non-monotonic folding of some proteins in aqueous DESs. A major thermal stability enhancement in the DES is also observed, caused by a similar slowdown of the backbone torsional dynamics. Our results support a kinetic stabilization of the protein in the DES, whereas a possible thermodynamic stabilization does not follow a preferential hydration or water entrapment mechanism.
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Affiliation(s)
- Inês Gomes
- BioISI-Biosystems and Integrative Sciences Institute, Faculty of Sciences of the University of Lisbon, C8, Campo Grande, 1749-016 Lisbon, Portugal
| | - Nuno Galamba
- BioISI-Biosystems and Integrative Sciences Institute, Faculty of Sciences of the University of Lisbon, C8, Campo Grande, 1749-016 Lisbon, Portugal
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3
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Eronina TB, Mikhaylova VV, Chebotareva NA, Kleymenov SY, Pivovarova AV, Kurganov BI. Combined action of chemical chaperones on stability, aggregation and oligomeric state of muscle glycogen phosphorylase b. Int J Biol Macromol 2022; 203:406-416. [PMID: 35066023 DOI: 10.1016/j.ijbiomac.2022.01.106] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/10/2022] [Accepted: 01/17/2022] [Indexed: 01/19/2023]
Abstract
Chemical chaperones are a class of small molecules, which enhance protein stability, folding, inhibit protein aggregation, and are used for long-term storage of therapeutic proteins. The combined action of chemical chaperones trehalose, betaine and lysine on stability, aggregation and oligomeric state of muscle glycogen phosphorylase b (Phb) has been studied. Dynamic light scattering data indicate that the affinity of trehalose to Phb increased in the presence of betaine or lysine at both stages (stage of nucleation and aggregate growth) of enzyme aggregation at 48 °C, in contrast, the affinity of betaine to the enzyme in the presence of lysine remained practically unchanged. According to differential scanning calorimetry and analytical ultracentrifugation data, the mixture of trehalose and betaine stabilized Phb stronger than either of them in total. Moreover, the destabilizing effect of lysine on the enzyme was almost completely compensated by trehalose and only partially by betaine. The main protective effect of the mixtures of osmolytes and lysine is associated with their influence on the dissociation/denaturation stage, which is the rate-limiting one of Phb aggregation. Thus, a pair of chaperones affects the stability, oligomeric state, and aggregation of Phb differently than individual chaperones.
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Affiliation(s)
- Tatiana B Eronina
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Leninsky pr. 33, Moscow 119071, Russia.
| | - Valeriya V Mikhaylova
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Leninsky pr. 33, Moscow 119071, Russia
| | - Natalia A Chebotareva
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Leninsky pr. 33, Moscow 119071, Russia
| | - Sergey Y Kleymenov
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Leninsky pr. 33, Moscow 119071, Russia; Koltsov's Institute of Developmental Biology, Russian Academy of Sciences, Vavilova 26, Moscow 119991, Russia
| | - Anastasia V Pivovarova
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Leninsky pr. 33, Moscow 119071, Russia
| | - Boris I Kurganov
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Leninsky pr. 33, Moscow 119071, Russia
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4
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Paul S, Paul S. Molecular insights into the urea-choline- O-sulfate interactions in aqueous solution. Phys Chem Chem Phys 2021; 23:25317-25334. [PMID: 34747954 DOI: 10.1039/d1cp02821a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Urea and choline-O-sulfate (COS) are both osmolytes, but have opposite effects on protein structure. Urea has been well-known for years to destabilize protein structure. Though COS has been revealed as an osmoprotective molecule against urea induced denaturation of proteins, the mechanism of this compensation is still unexplored. This study focuses on a theoretical investigation of the interdependent behavior of urea and COS in a mixture, to explore how urea becomes a weaker denaturing agent in the presence of COS. In this study, we have considered every possible interaction among the solute (urea and COS) and solvent (water) both at room temperature and high temperature, employing two different force field parameters i.e., CHARMM General Force Field parameters (CGenFF) and General AMBER Force Field (GAFF) parameters through classical molecular dynamics simulation studies. Different techniques have been used to analyze the average interactions between COS and urea as well as their solvation properties, which show that in the presence of COS, urea becomes a less effective denaturant than when alone. The water-water interaction shows that the mixed osmolyte solution of urea and COS strengthens the water hydrogen bonding network. The enhanced solvation of urea and COS in the urea-COS mixture and their mutual interactions, results in the exclusion of free urea as well as COS from the solution. This synergistic behavior of urea and COS could be the major reason behind COS counteracting urea's denaturation of proteins.
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Affiliation(s)
- Srijita Paul
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India.
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India.
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5
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Mojtabavi S, Jafari M, Samadi N, Mehrnejad F, Ali Faramarzi M. Insights into the Molecular-Level details of betaine interactions with Laccase under various thermal conditions. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116832] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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6
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Cozzolino S, Tortorella A, Del Vecchio P, Graziano G. General Counteraction Exerted by Sugars against Denaturants. Life (Basel) 2021; 11:652. [PMID: 34357025 PMCID: PMC8303697 DOI: 10.3390/life11070652] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 11/16/2022] Open
Abstract
The conformational stability of globular proteins is strongly influenced by the addition to water of different co-solutes. Some of the latter destabilize the native state, while others stabilize it. It is emerging that stabilizing agents are able to counteract the action of destabilizing agents. We have already provided experimental evidence that this counteraction is a general phenomenon and offered a rationalization. In the present work, we show that four different sugars, namely fructose, glucose, sucrose, and trehalose, counteract the effect of urea, tetramethylurea, sodium perchlorate, guanidinium chloride, and guanidinium thiocyanate despite the chemical and structural differences of those destabilizing agents. The rationalization we provide is as follows: (a) the solvent-excluded volume effect, a purely entropic effect, stabilizes the native state, whose solvent-accessible surface area is smaller than the one of denatured conformations; (b) the magnitude of the solvent-excluded volume effect increases markedly in ternary solutions because the experimental density of such solutions is larger than that of pure water.
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Affiliation(s)
- Serena Cozzolino
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, 80126 Napoli, Italy; (S.C.); (A.T.); (P.D.V.)
| | - Attila Tortorella
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, 80126 Napoli, Italy; (S.C.); (A.T.); (P.D.V.)
| | - Pompea Del Vecchio
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, 80126 Napoli, Italy; (S.C.); (A.T.); (P.D.V.)
| | - Giuseppe Graziano
- Dipartimento di Scienze e Tecnologie, Università degli Studi del Sannio, Via Francesco de Sanctis snc, 82100 Benevento, Italy
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7
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Affiliation(s)
- Yuri Shakhman
- Institute of Chemistry and The Fritz Haber Research Center Edmond J. Safra Campus The Hebrew University Jerusalem 9190401 Israel
| | - Daniel Harries
- Institute of Chemistry and The Fritz Haber Research Center Edmond J. Safra Campus The Hebrew University Jerusalem 9190401 Israel
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8
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Acharyya A, Shin D, Troxler T, Gai F. Can glycine betaine denature proteins? Phys Chem Chem Phys 2020; 22:7794-7802. [PMID: 32242578 DOI: 10.1039/d0cp00397b] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Glycine betaine (GB) is a naturally occurring osmolyte that has been widely recognized as a protein protectant. Since GB consists of a methylated ammonium moiety, it can engage in strong cation-π interactions with aromatic amino acid sidechains. We hypothesize that such specific binding interactions would allow GB to decrease the stability of proteins that are predominantly stabilized by a cluster of aromatic amino acids. To test this hypothesis, we investigate the effect of GB on the stability of two β-hairpins (or mini-proteins) that contain such a cluster. We find that for both systems the stability of the folded state first decreases and then increases with increasing GB concentration. Such non-monotonic dependence not only confirms that GB can act as a protein denaturant, but also underscores the complex interplay between GB's stabilizing and destabilizing forces toward a given protein. While stabilizing osmolytes all have the tendency to be excluded from the protein surface which is the action underlying their stabilizing effect, our results suggest that in order to quantitatively assess the effect of GB on the stability of any given protein, specific cation-π binding interactions need to be explicitly considered. Moreover, our results show, consistent with other studies, that cation methylation can strengthen the respective cation-π interactions. Taken together, these findings provide new insight into the mechanism by which amino acid-based osmolytes interact with proteins.
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Affiliation(s)
- Arusha Acharyya
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104, USA.
| | - Dayoung Shin
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104, USA.
| | - Thomas Troxler
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104, USA.
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104, USA.
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9
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Anumalla B, Prabhu NP. Surface hydration and preferential interaction directs the charged amino acids-induced changes in protein stability. J Mol Graph Model 2020; 98:107602. [PMID: 32251994 DOI: 10.1016/j.jmgm.2020.107602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 03/20/2020] [Accepted: 03/23/2020] [Indexed: 01/23/2023]
Abstract
In the present study, we investigate the interaction of amino acid osmolytes, Arg, Lys, Asp and Glu, and a denaturant, guanidinium chloride (Gdm) with proteins. To achieve this, molecular dynamics (MD) simulation of RNase A and α-lactalbumin was performed in the presence of three charged amino acids Arg, Lys, and Asp and the molecular mechanism of amino acid-induced (de)stabilization of the proteins was examined by combining with our earlier report on Glu. As Arg has the side chain similar to that of Gdm and destabilizes the proteins, MD simulation was carried out in the presence of Gdm as well. Radial distribution function and hydration fraction around the protein surface reveals that preferential hydration increases upon the addition of any of the cosolvent; however, the extent of increase is more in the presence of stabilizing cosolvents (stAAs: Lys, Asp and Glu) compared to destabilizing cosolvents (Arg and Gdm). Moreover, the preferential interaction of Arg and Gdm with the proteins is higher than that of stAAs. Residue-level interaction analysis suggests that stAAs preferably interacts with charged amino acids of the proteins whereas Arg and Gdm interactions could be found on almost all the surface exposed residues which might provide higher preferential interaction for these residues. From the results, we propose that the net outcome of preferential hydration versus preferential interaction of the amino acids might determine their effect on the stability of proteins.
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Affiliation(s)
- Bramhini Anumalla
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, 500 046, India
| | - N Prakash Prabhu
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, 500 046, India.
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10
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Chettiyankandy P, Chowdhuri S. Ion solvation scenario in an aqueous solution mixture of counteracting osmolytes: Urea and trimethylamine-N-oxide (TMAO). J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111467] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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11
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Mohan V, Sengupta B, Das N, Banerjee I, Sen P. Domain-Specific Stabilization of Structural and Dynamic Responses of Human Serum Albumin by Sucrose. Protein Pept Lett 2019; 26:287-300. [DOI: 10.2174/0929866526666190122115702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 01/03/2019] [Accepted: 01/12/2019] [Indexed: 11/22/2022]
Abstract
Background:Human Serum Albumin (HSA) is the most abundant protein present in human blood plasma. It is a large multi-domain protein with 585 amino acid residues. Due to its importance in human body, studies on the interaction of HSA with different external agent is of vital interest. The denaturation and renaturation of HSA in presence of external agents are of particular interest as they affect the biological activity of the protein.Objective:The objective of this work is to study the domain-specific and overall structural and dynamical changes occurring to HSA in the presence of a denaturing agent, urea and a renaturing agent, sucrose.Methods:In order to carry out the domain-specific studies, HSA has been tagged using N-(7- dimethylamino-4-methylcoumarin-3-yl) iodoacetamide (DACIA) at Cys-34 of domain-I and pnitrophenyl coumarin ester (NPCE) at Tyr-411 site in domain-III, separately. Steady-state absorption, emission and solvation dynamic measurements have been carried out in order to monitor the domain-specific alteration of HSA caused by the external agents. The overall structural change of HSA have been monitored using circular dichroism spectroscopy.Results:The α-helicity of HSA was found to decrease from 65% to 11% in presence of urea and was found to further increase to 25% when sucrose is added, manifesting the denaturing and renaturing effects of urea and sucrose, respectively. The steady state studies show that domain-III is more labile towards denaturation as compared to domain-I. The presence of an intermediate state is observed during the denaturation process. The stabilization of this intermediate state in presence of sucrose is attributed as the reason for the stabilization of HSA by sucrose. From solvation dynamics studies, it could be seen that the solvation time of DACIA inside domain-I of HSA decreases and increases regularly with increasing concentrations of urea and sucrose, respectively, while in the case of NPCE-tagged domain-III, the effect of sucrose on solvation time is evident only at high concentrations of urea.Conclusion:The denaturing and renaturing effects of urea and sucrose could be clearly seen from the steady state studies and circular dichroism spectroscopy measurements. A regular change in solvation time could only be observed in the case of domain-I and not in domain-III. The results indicate that the renaturing effect of sucrose on domain-III is not very evident when protein is in its native state, but is evident in when the protein is denatured.</P>
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Affiliation(s)
- Vaisakh Mohan
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur - 208 016, UP, India
| | - Bhaswati Sengupta
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur - 208 016, UP, India
| | - Nilimesh Das
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur - 208 016, UP, India
| | - Indrani Banerjee
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur - 208 016, UP, India
| | - Pratik Sen
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur - 208 016, UP, India
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12
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Olivares B, Martínez F, Rivas L, Calderón C, M Munita J, R Campodonico P. A Natural Deep Eutectic Solvent Formulated to Stabilize β-Lactam Antibiotics. Sci Rep 2018; 8:14900. [PMID: 30297853 PMCID: PMC6175898 DOI: 10.1038/s41598-018-33148-w] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 09/19/2018] [Indexed: 01/26/2023] Open
Abstract
β-lactam antibiotics, such as penicillin share a very unstable chemical structure. In water-based solutions, such as those used for clinical applications, the β-lactam ring is readily opened due to a nucleophilic or electrophilic attack, leading to the loss of antimicrobial activity. Since the achievement and maintenance of optimum therapeutic levels of β-lactam antibiotics is critical for the resolution of many infectious clinical situations, and to avoid antibiotic resistance generation, the design of new non-aqueous dosage forms is urgent. Recently, natural deep eutectic solvents (NADES) have emerged as alternative non-toxic and non-aqueous solvents for different biomedical applications. In this work, we formulated and characterized a NADES composed by betaine and urea (BU). Using this solvent, we evaluated the stability of clavulanic acid (CLV) and imipenem (IMP) and characterized their antimicrobial activities calculating the minimal inhibitory concentration. Characterization of BU solvent by infrared spectroscopy (IR) and nuclear magnetic resonance spectroscopy (NMR) indicated that the obtained solvent has a microstructure mainly based on hydrogen bonding interactions and water addition strongly affects its dynamic. The stability of β-lactam antibiotic IMP and CLV using this solvent was increased by 7 fold and 2.5 fold respectively compared to water when analysed seven days after being dissolved. Microbiological assays showed that antibacterial activity at day seven was significantly decreased for both CLV and IMP when dissolved in water, while no change in their antibacterial properties was observed when antibiotics were dissolved in BU. The increased stability of IMP and CLV in BU may be related to the inert behaviour of the solvent and the higher dynamic restriction that helps antibiotics to maintain a more stable conformation. These data suggest the potential use of BU as a solvent to prevent degradation of β-lactam antibiotics.
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Affiliation(s)
- Belén Olivares
- Centro de Química Médica, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile. .,Programa de Postgrado en Biología, Universidad Nacional de Cuyo, Mendoza, Argentina.
| | - Fabián Martínez
- Centro de Química Médica, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Lina Rivas
- Programa de Genómica y Resistencia Microbiana, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Cristian Calderón
- Centro de Química Médica, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - José M Munita
- Programa de Genómica y Resistencia Microbiana, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile.,Millennium Nucleus on Interdisciplinary Approach to Antimicrobial Resistance, Santiago, Chile
| | - Paola R Campodonico
- Centro de Química Médica, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
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Paul S, Paul S. How Does Aqueous Choline-O-Sulfate Solution Nullify the Action of Urea in Protein Denaturation? J Chem Inf Model 2018; 58:1858-1869. [DOI: 10.1021/acs.jcim.8b00395] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Srijita Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam, India−781039
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam, India−781039
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14
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Borgohain G, Paul S. Atomistic level understanding of the stabilization of protein Trp cage in denaturing and mixed osmolyte solutions. COMPUT THEOR CHEM 2018. [DOI: 10.1016/j.comptc.2018.03.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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15
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El-Chami C, Haslam IS, Steward MC, O'Neill CA. Organic osmolytes preserve the function of the developing tight junction in ultraviolet B-irradiated rat epidermal keratinocytes. Sci Rep 2018; 8:5167. [PMID: 29581434 PMCID: PMC5979960 DOI: 10.1038/s41598-018-22533-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 02/08/2018] [Indexed: 01/04/2023] Open
Abstract
Epidermal barrier function is provided by the highly keratinised stratum corneum and also by tight junctions (TJs) in the granular layer of skin. The development of the TJ barrier significantly deteriorates in response to ultraviolet B radiation (UVB). Following exposure to UVB, keratinocytes accumulate organic osmolytes, which are known to preserve cell volume during water stress. Since TJs are intimately associated with control of water homeostasis in skin, we hypothesised that there may be a direct influence of osmolytes on TJ development. Exposure of rat epidermal keratinocytes (REKs) to a single dose of UVB reduced the function of developing TJs. This was concomitant with dislocalisation of claudin-1 and claudin-4 from the keratinocyte plasma membrane, phosphorylation of occludin and elevation of reactive oxygen species (ROS). In the presence of organic osmolytes, these effects were negated but were independent of the effects of these molecules on cell volume, elevation of ROS or the gene expression of TJ proteins. These data suggest that organic osmolytes affect TJs via post-translational mechanism(s) possibly involving protection of the native conformation of TJ proteins.
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Affiliation(s)
- Cécile El-Chami
- School of Biological Sciences, Division of Musculoskeletal & Dermatological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, M13 9PT, United Kingdom
| | - Iain S Haslam
- School of Biological Sciences, Division of Musculoskeletal & Dermatological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, M13 9PT, United Kingdom.,School of Medical Sciences, Division of Diabetes, Endocrinology and Gastroenterology, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, M13 9PT, United Kingdom.,Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, United Kingdom
| | - Martin C Steward
- School of Medical Sciences, Division of Diabetes, Endocrinology and Gastroenterology, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, M13 9PT, United Kingdom
| | - Catherine A O'Neill
- School of Biological Sciences, Division of Musculoskeletal & Dermatological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, M13 9PT, United Kingdom.
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Meti MD, Dixit MK, Tembe BL. Salting-in of neopentane in the aqueous solutions of urea and glycine-betaine. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1431834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Manjunath D. Meti
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Mayank K. Dixit
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Bhalachandra L. Tembe
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, India
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17
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Hwang MP, Ding X, Gao J, Acharya AP, Little SR, Wang Y. A biocompatible betaine-functionalized polycation for coacervation. SOFT MATTER 2018; 14:387-395. [PMID: 29147712 PMCID: PMC5771809 DOI: 10.1039/c7sm01763d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The aqueous nature of complex coacervates provides a biologically-relevant context for various therapeutic applications. In this sense, biological applications demand a corresponding level of biocompatibility from the polyelectrolytes that participate in complex coacervation. Continued development with naturally-occurring polyelectrolytes such as heparin and chitosan underscore such aims. Herein, we design a synthetic polycation, in which betaine is conjugated to a biodegradable polyester backbone. Betaine is a naturally-occurring methylated amino acid that is ubiquitously present in human plasma. Inspired by its vast range of benefits - including but not limited to anti-inflammation, anti-cancer, anti-bacterial, anti-oxidant, protein stabilization, and cardiovascular health - we aim to impart additional functionality to a polycation for eventual use in a complex coacervate with heparin. We report on its in vitro and in vivo biocompatibility, in vitro and in vivo effect on angiogenesis, in vitro effect on microbial growth, and ability to form complex coacervates with heparin.
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Affiliation(s)
- Mintai P Hwang
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA.
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18
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Ghosh S, Dey S, Patel M, Chakrabarti R. Can an ammonium-based room temperature ionic liquid counteract the urea-induced denaturation of a small peptide? Phys Chem Chem Phys 2017; 19:7772-7787. [DOI: 10.1039/c6cp08842b] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The folding/unfolding equilibrium of proteins in aqueous medium can be altered by adding small organic molecules generally termed as co-solvents.
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Affiliation(s)
- Soumadwip Ghosh
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai – 400076
- India
| | - Souvik Dey
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai – 400076
- India
| | - Mahendra Patel
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai – 400076
- India
| | - Rajarshi Chakrabarti
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai – 400076
- India
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19
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Sarkar S, Ghosh S, Chakrabarti R. Ammonium based stabilizers effectively counteract urea-induced denaturation in a small protein: insights from molecular dynamics simulations. RSC Adv 2017. [DOI: 10.1039/c7ra10712a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Room temperature ionic liquids (IL) and deep eutectic solvents (DES) are known to aid the conformational stability and activity of proteins and enzymes in aqueous solutions.
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Affiliation(s)
- Soham Sarkar
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai – 400076
- India
| | - Soumadwip Ghosh
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai – 400076
- India
| | - Rajarshi Chakrabarti
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai – 400076
- India
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20
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Ishtikhar M, Rahisuddin, Khan MV, Khan RH. Anti-aggregation property of thymoquinone induced by copper-nanoparticles: A biophysical approach. Int J Biol Macromol 2016; 93:1174-1182. [DOI: 10.1016/j.ijbiomac.2016.09.089] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 09/24/2016] [Accepted: 09/26/2016] [Indexed: 12/14/2022]
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21
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Zeng CX, Qi SJ, Xin RP, Yang B, Wang YH. Synergistic behavior of betaine–urea mixture: Formation of deep eutectic solvent. J Mol Liq 2016. [DOI: 10.1016/j.molliq.2016.02.076] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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22
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Fonin AV, Uversky VN, Kuznetsova IM, Turoverov KK. Protein folding and stability in the presence of osmolytes. Biophysics (Nagoya-shi) 2016. [DOI: 10.1134/s0006350916020056] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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23
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Effect of glycine betaine on the hydrophobic interactions in the presence of denaturant: A molecular dynamics study. J Mol Liq 2016. [DOI: 10.1016/j.molliq.2015.12.037] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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24
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Dixit MK, Siddique AA, Tembe BL. Salting-Out of Methane in the Aqueous Solutions of Urea and Glycine-Betaine. J Phys Chem B 2015; 119:10941-53. [PMID: 25965507 DOI: 10.1021/acs.jpcb.5b00556] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have studied the hydrophobic association and solvation of methane molecules in aqueous solutions of urea and glycine betaine (GB). We have calculated the potentials of mean force (PMFs) between methane molecules in water, aqueous GB, aqueous urea and aqueous urea-GB mixtures. The PMFs and equilibrium constants indicate that both urea and GB increase the hydrophobic association of methane. Calculation of thermodynamic parameters shows that the association of methane is stabilized by entropy whereas solvation is favored by enthalpy. In the case of the water-urea-GB mixture, both hydrophobic association and solvation are stabilized by entropy. From the investigation of radial distribution functions, running coordination numbers and excess coordination numbers, we infer that both urea and GB are preferentially excluded from methane surface in the mixtures of osmolytes and methane is preferentially solvated by water molecules in all the mixtures. The favorable exclusion of both urea and GB from the methane surface suggests that both urea and GB increase the interaction between methane molecules, i.e., salting-out of methane. We observe that addition of both urea and GB to water enhances local water structure. The calculated values of diffusion constants of water also suggest enhanced water-water interactions in the presence of urea and GB. The calculated free energies of methane in these mixtures show that methane is less soluble in the mixtures of urea and GB than in water. The data on solvation free energies support the observations obtained from the PMFs of methane molecules.
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Affiliation(s)
- Mayank Kumar Dixit
- Department of Chemistry, Indian Institute of Technology Bombay , Powai, Mumbai 400076, India
| | - Asrar A Siddique
- Department of Chemistry, Indian Institute of Technology Bombay , Powai, Mumbai 400076, India
| | - B L Tembe
- Department of Chemistry, Indian Institute of Technology Bombay , Powai, Mumbai 400076, India
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25
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Tekewe A, Connors NK, Sainsbury F, Wibowo N, Lua LH, Middelberg AP. A rapid and simple screening method to identify conditions for enhanced stability of modular vaccine candidates. Biochem Eng J 2015. [DOI: 10.1016/j.bej.2015.04.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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26
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Zeng CX, Qi SJ, Xin RP, Yang B, Wang YH. Enzymatic selective synthesis of 1,3-DAG based on deep eutectic solvent acting as substrate and solvent. Bioprocess Biosyst Eng 2015. [DOI: 10.1007/s00449-015-1445-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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27
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Paul S, Paul S. Investigating the Counteracting Effect of Trehalose on Urea-Induced Protein Denaturation Using Molecular Dynamics Simulation. J Phys Chem B 2015; 119:10975-88. [DOI: 10.1021/acs.jpcb.5b01457] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Subrata Paul
- Department
of Chemistry, Indian Institute of Technology, Guwahati, Assam India-781039
| | - Sandip Paul
- Department
of Chemistry, Indian Institute of Technology, Guwahati, Assam India-781039
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28
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Kumar N, Kishore N. Mechanistic insights into osmolyte action in protein stabilization under harsh conditions: N-methylacetamide in glycine betaine–urea mixture. Chem Phys 2014. [DOI: 10.1016/j.chemphys.2014.09.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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