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Manning MC, Holcomb RE, Payne RW, Stillahn JM, Connolly BD, Katayama DS, Liu H, Matsuura JE, Murphy BM, Henry CS, Crommelin DJA. Stability of Protein Pharmaceuticals: Recent Advances. Pharm Res 2024; 41:1301-1367. [PMID: 38937372 DOI: 10.1007/s11095-024-03726-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 06/03/2024] [Indexed: 06/29/2024]
Abstract
There have been significant advances in the formulation and stabilization of proteins in the liquid state over the past years since our previous review. Our mechanistic understanding of protein-excipient interactions has increased, allowing one to develop formulations in a more rational fashion. The field has moved towards more complex and challenging formulations, such as high concentration formulations to allow for subcutaneous administration and co-formulation. While much of the published work has focused on mAbs, the principles appear to apply to any therapeutic protein, although mAbs clearly have some distinctive features. In this review, we first discuss chemical degradation reactions. This is followed by a section on physical instability issues. Then, more specific topics are addressed: instability induced by interactions with interfaces, predictive methods for physical stability and interplay between chemical and physical instability. The final parts are devoted to discussions how all the above impacts (co-)formulation strategies, in particular for high protein concentration solutions.'
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Affiliation(s)
- Mark Cornell Manning
- Legacy BioDesign LLC, Johnstown, CO, USA.
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA.
| | - Ryan E Holcomb
- Legacy BioDesign LLC, Johnstown, CO, USA
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
| | - Robert W Payne
- Legacy BioDesign LLC, Johnstown, CO, USA
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
| | - Joshua M Stillahn
- Legacy BioDesign LLC, Johnstown, CO, USA
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
| | | | | | | | | | | | - Charles S Henry
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
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2
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Baruah I, Borgohain G. Temperature dependent molecular dynamics simulation study to understand the stabilizing effect of NADES on the protein β-Lactoglobulin. J Mol Graph Model 2023; 125:108582. [PMID: 37595383 DOI: 10.1016/j.jmgm.2023.108582] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 07/24/2023] [Accepted: 07/28/2023] [Indexed: 08/20/2023]
Abstract
The thermal stability of a protein is an important concern for its practical application in food processing industries. In this study, we have carried out classical molecular dynamics simulations to systematically investigate the effect of NADES (natural deep eutectic solvent) on the stabilization of the protein β-Lactoglobulin (BLG) at different temperatures. This study sheds light on the very aspects of NADES composed of betaine and sorbitol on the stability of the protein. NADES provides better stability to the protein up to a temperature of 400 K than in water. It is observed that the protein starts to unfold above temperature 400 K in spite of the presence of NADES which is quiet evident from the root mean square deviation (RMSD) and radius of gyration (Rg) plots. The decreasing average solvent accessible surface area (SASA) values and increasing intra-protein hydrogen bonds indicate better stability of the protein in NADES medium than in water at temperatures 300 K and 400 K. At high temperatures viz. 450 K and 500 K the number and distribution of solvent species (betaine and sorbitol) around the protein surface show an increment that are evident from the calculations of solvation shell, radial and spatial distribution functions. Increased number of betaine molecules that interact with the protein through electrostatic interaction may lead to destabilization of the protein at these temperatures. This study suggests that NADES could be used as an ideal medium for thermal stability of the protein BLG up to a temperature of 400 K. Beyond this temperature, NADES used for this study fails to exert stabilization effect on the protein.
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Affiliation(s)
- Indrani Baruah
- Department of Chemistry, Cotton University, Guwahati, Assam, 781001, India
| | - Gargi Borgohain
- Department of Chemistry, Cotton University, Guwahati, Assam, 781001, India.
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3
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Ghanta KP, Bandyopadhyay S. Counteraction Effects of Ammonium-Based Ionic Liquids on Urea-Induced Denaturation of α-Lactalbumin: A Comprehensive Molecular Simulation Study. J Phys Chem B 2023; 127:7251-7265. [PMID: 37574910 DOI: 10.1021/acs.jpcb.3c03223] [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: 08/15/2023]
Abstract
Ionic liquids (ILs) are known to stabilize protein conformations in aqueous medium. Importantly, ILs can also act as refolding additives in urea-driven denaturation of proteins. However, despite the importance of the problem, detailed microscopic understanding of the counteraction effects of ILs on urea-induced protein denaturation remains elusive. In this work, atomistic molecular dynamics (MD) simulations of the protein α-lactalbumin have been carried out in pure aqueous medium, in 8 M binary urea-water solution and in ternary urea-IL-water solutions containing ammonium-based ethyl ammonium acetate (EAA) as the IL at different concentrations (1-4 M). Attempts have been made to quantify detailed molecular-level understanding of the origin behind the counteraction effects of the IL on urea-induced partial unfolding of the protein. The calculations revealed significant conformational changes of the protein with multiple free energy minima due to its partial unfolding in binary urea-water solution. The counteraction effect of the IL was evident from the enhanced structural rigidity of the protein with propensity to transform into a single native free energy minimum state in ternary urea-IL-water solutions. Such an effect has been found to be associated with preferential direct binding of the IL components with the protein and simultaneous expulsion of urea from the interface, thereby providing additional stabilization of the protein in ternary solutions. Most importantly, modified rearrangement of the hydrogen bond network at the interface due to the formation of stronger protein-cation (PC) and protein-anion (PA) hydrogen bonds by breaking relatively weaker protein-urea (PU) and protein-water (PW) hydrogen bonds has been recognized as the microscopic origin behind the counteraction effects of EAA on urea-induced partial unfolding of the protein.
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Affiliation(s)
- Krishna Prasad Ghanta
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
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Khan A, Nayeem SM. Stability of the Aβ42 Peptide in Mixed Solutions of Denaturants and Proline. J Phys Chem B 2023; 127:1572-1585. [PMID: 36786778 DOI: 10.1021/acs.jpcb.2c08505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Amyloid β-peptide (Aβ) is responsible for the neuronal damage and death of a patient with Alzheimer's disease (AD). Aβ42 oligomeric forms are dominant neurotoxins and are related to neurodegeneration. Their different forms are related to various pathological conditions in the brain. We investigated Aβ42 peptides in different environments of proline, urea, and GdmCl solutions (in pure and mixed binary forms) through atomistic molecular dynamics simulations. Preferential exclusion from the protein surface and facile formation of a large number of weak molecular interactions are the driving forces for the osmolyte's action. We have focused on these interactions between peptide monomers and pure/mixed osmolytes and denaturants. Urea, as usual, denatures the peptide strongly compared to the GdmCl by accumulation around the peptide. GdmCl shows lesser build-up around protein in contrast to urea but is involved in destabilizing the salt bridge formation of Asp23 and Lys28. Proline as an osmolyte protects the peptide from aggregation when mixed with urea and GdmCl solutions. In mixed solutions of two denaturants and osmolyte plus denaturant, the peptide shows enhanced stability as compared to pure denaturant urea solution. The enhanced stability of peptides in proline may be attributed to its exclusion from the peptide surface and favoring salt bridge formation.
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Affiliation(s)
- Ashma Khan
- Department of Chemistry, Aligarh Muslim University, Aligarh 202002, UP, India
| | - Shahid M Nayeem
- Department of Chemistry, Aligarh Muslim University, Aligarh 202002, UP, India
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Gazi R, Maity S, Jana M. Conformational Features and Hydration Dynamics of Proteins in Cosolvents: A Perspective from Computational Approaches. ACS OMEGA 2023; 8:2832-2843. [PMID: 36713749 PMCID: PMC9878537 DOI: 10.1021/acsomega.2c08009] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 12/22/2022] [Indexed: 06/18/2023]
Abstract
The importance of solvent in stabilizing protein structures has long been recognized. Water is the common solvent for proteins, and hydration is elemental in governing protein stability, flexibility, and function through various interactions. The addition of small organic molecules known as cosolvents may deploy stabilization (folding) or destabilization (unfolding) effects on native protein conformations. Despite exhaustive literature, the molecular mechanism by which cosolvents regulate protein conformations and dynamics is controversial. Specifically, the cosolvent behavior has been unpredictable with the nature and concentrations that lead to protein stabilizing/destabilizing effects as it changes in water content near the vicinity of proteins. With the massive development of computational resources, advancement of computational methods, and the availability of numerous experimental techniques, various theoretical and computational studies of proteins in a mixture of solvents have been instigated. The growing interest in such studies has been to unravel the underlying mechanism of protein folding and cosolvent/solvent-protein interactions that have significant implications in biomedical and biotechnological applications. In this mini-review, apart from the brief overview of important theories and force-field model-based cosolvent effects on proteins, we present the current state of knowledge and recent advances in the field to describe cosolvent-guided conformational features of proteins and hydration dynamics from computational approaches. The mini-review further explains the mechanistic details of protein stability in various popularly used cosolvents, including limitations of present studies and future outlooks. The counteracting effects of cosolvent on the proteins in the mixture of stabilizing and destabilizing cosolvents are also presented and discussed.
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Chen N, Zhang X, Lyu J, Zhao G, Gu K, Xia J, Chen Z, Shao Z. Preparation of a novel regenerated silk fibroin-based hydrogel for extrusion bioprinting. SOFT MATTER 2022; 18:7360-7368. [PMID: 36124911 DOI: 10.1039/d2sm00984f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Three-dimensional (3D) bioprinting technology, allowing rapid prototyping and personalized customization, has received much attention in recent years, while regenerated silk fibroin (RSF) has also been widely investigated for its excellent biocompatibility, processibility, and comprehensive mechanical properties. However, due to the difficulty in curing RSF aqueous solution and the tendency of conformational transition of RSF chains under shearing, it is rather complicated to fabricate RSF-based materials with high mechanical strength through extrusion bioprinting. To solve this problem, a printable hydrogel with thixotropy was prepared from regenerated silk fibroin with high-molecular-weight (HMWRSF) combined with a small amount of hydroxypropyl methylcellulose (HPMC) in urea containing aqueous solution. It was found that the introduction of urea could not only vary the solid content of the hydrogel to benefit the mechanical properties of the 3D-bioprinted pre-cured hydrogels or 3D-bioprinted sponges, but also expand the "printable window" of this system. Indeed, the printability and rheological properties could be modulated by varying the solid content, the heating time, the urea/HMWRSF weight ratio, etc. Moreover, the microstructure of nanospheres stacked in these lyophilized 3D-bioprinted sponges was interesting to observe, which indicated the existence of microhydrogels and both "the reversible network" and "the irreversible network" in this HMWRSF-based pre-cured hydrogel. Like other HMWRSF materials fabricated in other ways, these 3D-bioprinted HMWRSF-based sponges exhibited good cytocompatibility for dental pulp mesenchymal stem cells. This work may inspire the design of functional HMWRSF-based materials by regulating the relationship between structure and properties.
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Affiliation(s)
- Ni Chen
- State Key Laboratory of Molecular Engineering of Polymers, Laboratory of Advanced Materials and Department of Macromolecular Science, Fudan University, Shanghai 200433, P. R. China.
| | - Xinbo Zhang
- Department of Materials Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, P. R. China
| | - Jinyang Lyu
- Department of Orthopedic Surgery, Huashan Hospital, Fudan University, Shanghai 200040, P. R. China
| | - Guanglei Zhao
- Department of Orthopedic Surgery, Huashan Hospital, Fudan University, Shanghai 200040, P. R. China
| | - Kai Gu
- State Key Laboratory of Molecular Engineering of Polymers, Laboratory of Advanced Materials and Department of Macromolecular Science, Fudan University, Shanghai 200433, P. R. China.
| | - Jun Xia
- Department of Orthopedic Surgery, Huashan Hospital, Fudan University, Shanghai 200040, P. R. China
| | - Zhongchun Chen
- Department of Otorhinolaryngology-Head and Neck Surgery, Huashan Hospital, Fudan University, Shanghai 200040, P. R. China
| | - Zhengzhong Shao
- State Key Laboratory of Molecular Engineering of Polymers, Laboratory of Advanced Materials and Department of Macromolecular Science, Fudan University, Shanghai 200433, P. R. China.
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Nanavare P, Choudhury AR, Sarkar S, Maity A, Chakrabarti R. Structure and Orientation of Water and Choline Chloride Molecules Around a Methane Hydrophobe: A Computer Simulation Study. Chemphyschem 2022; 23:e202200446. [DOI: 10.1002/cphc.202200446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/18/2022] [Indexed: 11/12/2022]
Affiliation(s)
- Pooja Nanavare
- IIT Bombay: Indian Institute of Technology Bombay Department of Chemistry INDIA
| | - Asha Rani Choudhury
- IIT Bombay: Indian Institute of Technology Bombay Department of Chemistry INDIA
| | - Soham Sarkar
- TU Darmstadt: Technische Universitat Darmstadt Eduard-Zintl-Institute für Anorganische und Physikalische Chemie INDIA
| | - Atanu Maity
- IIT Bombay: Indian Institute of Technology Bombay Department of Chemistry INDIA
| | - Rajarshi Chakrabarti
- Indian Institute of Technology Bombay Chemistry Indian Institute of Technology BombayPowaiIndia 400076 Mumbai INDIA
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8
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In silico studies of the human IAPP in the presence of osmolytes. J Mol Model 2022; 28:188. [PMID: 35697975 DOI: 10.1007/s00894-022-05180-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 05/30/2022] [Indexed: 10/18/2022]
Abstract
The human islet amyloid polypeptide or amylin is secreted along with insulin by pancreatic islets. Under the drastic environmental conditions, amylin can aggregate to form amyloid fibrils. This amyloid plaque of hIAPP in the pancreatic cells is the cause of type II diabetes. Early stages of amylin aggregates are more cytotoxic than the matured fibrils. Here, we have used the all-atom molecular dynamic simulation to see the effect of water, TMAO, urea and urea/TMAO having ratio 2:1 of different concentrations on the amylin protein. Our study suggest that the amylin protein forms β-sheets in its monomeric form and may cause the aggregation of protein through the residue 13-17 and the C-terminal region. α-Helical content of protein increases with an increase in TMAO concentration by decreasing the SASA value of protein, increase in intramolecular hydrogen bonds and on making the short-range hydrophobic interactions. Electrostatic potential surfaces show that hydrophobic groups are buried and normalised configurational entropy of backbone, and side-chain atoms is lesser in the presence of TMAO, whereas opposite behaviour is obtained in the case of urea. Counteraction effect of TMAO using Kast model towards urea is also observed in ternary solution of urea/TMAO.
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Rahman MH, Senapati S. Effects of Ionic Liquids on Aqueous Urea Solutions: Insights into the Ionic Liquid-Assisted Protein Renaturation. J Phys Chem B 2021; 125:4808-4818. [PMID: 33914552 DOI: 10.1021/acs.jpcb.1c00586] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ionic liquids (ILs) are designer solvents that find wide applications in various areas. Recently, ILs have been shown to induce the refolding of certain proteins that were previously denatured under the treatment of urea. A molecular-level understanding of the counteracting mechanism of ILs on urea-induced protein denaturation remains elusive. In this study, we employ atomistic molecular dynamics simulations to investigate the ternary urea-water-IL solution in comparison to the aqueous urea solution to understand how the presence of ILs can modulate the structure, energetics, and dynamics of urea-water solutions. Our results show that the ions of the IL used, ethylammonium nitrate (EAN), interact strongly with urea and disrupt the urea aggregates that were known to stabilize the unfolded state of the proteins. Results also suggest a disruption in urea-water interaction that releases more free water molecules in solution. We subsequently strengthened these findings by simulating a model peptide in the absence and presence of EAN, which showed broken versus intact secondary structure in urea solution. Analyses show that these changes were accomplished by the added IL, which enforced a gradual displacement of urea from the peptide surface by water. We propose that the ILs facilitate protein renaturation by breaking down the urea aggregates and increasing the amount of free water molecules around the protein.
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Affiliation(s)
- Mohammad Homaidur Rahman
- Department of Biotechnology, BJM School of Biosciences, Indian Institute of Technology Madras, Chennai 600 036, India
| | - Sanjib Senapati
- Department of Biotechnology, BJM School of Biosciences, Indian Institute of Technology Madras, Chennai 600 036, India
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Taherimehr Z, Zaboli M, Torkzadeh-Mahani M. New insight into the molecular mechanism of the trehalose effect on urate oxidase stability. J Biomol Struct Dyn 2020; 40:1461-1471. [PMID: 33000700 DOI: 10.1080/07391102.2020.1828167] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Urate oxidase (EC 1.7.3.3) is a key enzyme in the purine metabolism which is applied in the treatment of gout and also, as a diagnostic reagent for uric acid detection. In the current study, the trehalose (TRE) effects as an additive on the structural stability and function of uricase were investigated. For recombinant expression of UOX in E. coli BL21 cells, firstly the coding sequence was subcloned into the pET-28a vector and after induction with IPTG, the recombinant UOX was purified by affinity chromatography using a Ni-NTA agarose column. To specify the trehalose effects on the urate oxidase (UOX) structure, optimum pH, optimum temperature, kinetic and thermodynamic parameters and also, the intrinsic fluorescence of UOX in the absence and presence of trehalose were examined. The UOX half-life is 24.32 min at 40 °C, whereas the UOX-TRE has a higher half-life (32.09 min) at this temperature. Generally, our findings confirm that trehalose has a protective effect on the enzyme structure. Optimum pH and temperature were 9 and 25 °C, respectively for both the naked and treated enzymes and their activity retained 42.18 and 64.80%, respectively after 48 h of incubation at room temperature. Also, theoretical results indicate that the random coil of the enzyme was converted to α-helix and β-sheet in the presence of trehalose which may preserve the integrity of the active site of the enzyme and increased the enzymatic activity. The MD simulation results indicated greater stability of the uricase structure in the presence of trehalose.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Zahra Taherimehr
- Department of Biotechnology, Institute of Science, High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman-Iran, Iran
| | - Maryam Zaboli
- Department of chemistry, Faculty of science, University of Birjand, Birjand, Iran
| | - Masoud Torkzadeh-Mahani
- Department of Biotechnology, Institute of Science, High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman-Iran, Iran
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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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Attri P, Razzokov J, Yusupov M, Koga K, Shiratani M, Bogaerts A. Influence of osmolytes and ionic liquids on the Bacteriorhodopsin structure in the absence and presence of oxidative stress: A combined experimental and computational study. Int J Biol Macromol 2020; 148:657-665. [DOI: 10.1016/j.ijbiomac.2020.01.179] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/16/2020] [Accepted: 01/19/2020] [Indexed: 12/17/2022]
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Maity A, Sarkar S, Theeyancheri L, Chakrabarti R. Choline Chloride as a Nano‐Crowder Protects HP‐36 from Urea‐Induced Denaturation: Insights from Solvent Dynamics and Protein‐Solvent Interactions. Chemphyschem 2020; 21:552-567. [DOI: 10.1002/cphc.201901078] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 01/22/2020] [Indexed: 12/27/2022]
Affiliation(s)
- Atanu Maity
- Department of ChemistryIndian Institute of Technology Bombay Powai Mumbai 400076 India
| | - Soham Sarkar
- Department of ChemistryIndian Institute of Technology Bombay Powai Mumbai 400076 India
| | - Ligesh Theeyancheri
- Department of ChemistryIndian Institute of Technology Bombay Powai Mumbai 400076 India
| | - Rajarshi Chakrabarti
- Department of ChemistryIndian Institute of Technology Bombay Powai Mumbai 400076 India
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Nian B, Cao C, Liu Y. Synergistic Catalytic Synthesis of Gemini Lipoamino Acids Based on Multiple Hydrogen-Bonding Interactions in Natural Deep Eutectic Solvents-Enzyme System. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:989-997. [PMID: 31909616 DOI: 10.1021/acs.jafc.9b07446] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In the previous studies, gemini lipoamino acids (GLAA) were always synthesized by complex multistep organic synthesis, which involved a large number of byproducts and organic solvents. To develop a straightforward, efficient, and renewable synthesis strategy for GLAA, in this study, a type of novel green solvents, natural deep eutectic solvents (NADESs), were adopted as the solvents for these reactions. Five commercial enzymes were involved in the enzyme screening section, and Candida antarctica lipase B (CALB) tended to have the best performance in NADESs systems. The optimization procedure was performed using the Taguchi crossed array method and the highest yield of GLAA (59.14 ± 0.51%) was obtained in choline chloride-glycerol (C-Gly). The purification procedure was carried out with ethyl acetate and water, and the isolate yield ranged from 86.31 ± 2.36 to 91.34 ± 2.26%. With 10 times recycling, the yield of GLAA in C-Gly decreased from 59.14 ± 0.51 to 51.31 ± 0.68%. Interestingly, a synergistic effect of CALB and NADESs was found in the enzymatic synthesis of GLAA, which can be attributed to fatty acids being activated by chloride ions via hydrogen-bonding interactions and resulting in an enhancement in its electron-attracting ability.
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Affiliation(s)
- Binbin Nian
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province , Jiangnan University , 1800 Lihu Road , Wuxi , Jiangsu 214122 , People's Republic of China
| | - Chen Cao
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province , Jiangnan University , 1800 Lihu Road , Wuxi , Jiangsu 214122 , People's Republic of China
| | - Yuanfa Liu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province , Jiangnan University , 1800 Lihu Road , Wuxi , Jiangsu 214122 , People's Republic of China
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Abstract
The oligomerization of Aβ16-22 peptide, which is the hydrophobic core region of full-length Aβ1-42, causes Alzheimer's disease (AD). This progressive neurodegenerative disease affects over 44 million people worldwide. However, very few synthesized drug molecules are available to inhibit the aggregation of Aβ. Recently, experimental studies have shown that the biological ATP molecule prevents Aβ fibrillation at the millimolar scale; however, the significance of ATP molecules on Aβ fibrillation and the mechanism behind it remain elusive. We have carried out a total of 7.5 μs extensive all-atom molecular dynamics and 8.82 μs of umbrella sampling in explicit water using AMBER14SB, AMBER99SB-ILDN, and AMBER-FB15 force fields for Aβ16-22 peptide, to investigate the role of ATP on the disruption of Aβ16-22 prefibrils. From various analyses, such as secondary structure analysis, residue-wise contact map, SASA, and interaction energies, we have observed that, in the presence of ATP, the aggregation of Aβ16-22 peptide is very unfavorable. Moreover, the biological molecule ATP interacts with the Aβ16-22 peptide via hydrogen bonding, π-π stacking, and NH-π interactions which, ultimately, prevent the aggregation of Aβ16-22 peptide. Hence, we assume that the deficiency of ATP may cause Alzheimer's disease (AD).
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Affiliation(s)
- Saikat Pal
- Department of Chemistry , Indian Institute of Technology , Guwahati , Assam 781039 , India
| | - Sandip Paul
- Department of Chemistry , Indian Institute of Technology , Guwahati , Assam 781039 , India
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16
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Molecular level insight into the counteraction of trehalose on the activity as well as denaturation of lysozyme induced by guanidinium chloride. Chem Phys 2019. [DOI: 10.1016/j.chemphys.2019.110489] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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17
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Jahan I, Nayeem SM. Effect of Osmolytes on Conformational Behavior of Intrinsically Disordered Protein α-Synuclein. Biophys J 2019; 117:1922-1934. [PMID: 31699336 DOI: 10.1016/j.bpj.2019.09.046] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 09/21/2019] [Accepted: 09/30/2019] [Indexed: 11/20/2022] Open
Abstract
α-Synuclein is an intrinsically disordered protein whose function in a healthy brain is poorly understood. It is genetically and neuropathologically linked to Parkinson's disease (PD). PD is manifested after the accumulation of plaques of α-synuclein aggregates in the brain cells. Aggregates of α-synuclein are very toxic and lead to the disruption of cellular homeostasis and neuronal death. α-Synuclein can also contribute to disease propagation as it may exert noxious effects on neighboring cells. Understanding the mechanism of α-synuclein aggregation will facilitate the problem of dealing with neurodegenerative diseases in general and that of PD in particular. Here, we have used molecular dynamics simulations to investigate the behavior of α-synuclein at various temperatures and in different concentrations of urea and trimethyl amine oxide. The residue region from 61 to 95 of α-synuclein is experimentally known as amyloidogenic. In our study, we have identified some other regions, which also have the propensity to form an aggregate besides this known sequence. Urea being a denaturant interacts more with these regions of α-synuclein through hydrogen bond formation and inhibits the β-sheet formation, whereas trimethyl amine oxide itself does not interact much with the protein and stabilizes the protein by preferentially distributing water molecules on the surface of the protein.
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Affiliation(s)
- Ishrat Jahan
- Department of Chemistry, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Shahid M Nayeem
- Department of Chemistry, Aligarh Muslim University, Aligarh, Uttar Pradesh, India.
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18
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Das A, Basak P, Pramanick A, Majumder R, Pal D, Ghosh A, Guria M, Bhattacharyya M, Banik SP. Trehalose mediated stabilisation of cellobiase aggregates from the filamentous fungus Penicillium chrysogenum. Int J Biol Macromol 2019; 127:365-375. [PMID: 30658143 DOI: 10.1016/j.ijbiomac.2019.01.062] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 01/12/2019] [Accepted: 01/14/2019] [Indexed: 12/22/2022]
Abstract
Extracellular fungal cellobiases develop large stable aggregates by reversible concentration driven interaction. In-vitro addition of trehalose resulted in bigger cellobiase assemblies with increased stability against heat and dilution induced dissociation. In presence of 0.1 M trehalose, the size of aggregates increased from 344 nm to 494 nm. The increase in size was also observed in zymography of cellobiase. Activation energy of the trehalose stabilised enzyme (Ea = 220.9 kJ/mol) as compared to control (Ea = 257.734 kJ/mol), suggested enhanced thermostability and also showed increased resistance to chaotropes. Purified cellobiase was found to contain 196.27 μg of sugar/μg of protein. It was proposed that presence of glycan on protein's surface impedes and delays trehalose docking. Consequently, self-association of cellobiase preceded coating by trehalose leading to stabilisation of bigger cellobiase aggregates. In unison with the hypothesis, ribosylated BSA failed to get compacted by trehalose and developed into bigger aggregates with average size increasing from 210 nm to 328 nm. Wheat Germ Lectin, in presence of trehalose, showed higher molecular weight assemblies in DLS, native-PAGE and fluorescence anisotropy. This is the first report of cross-linking independent stabilisation of purified fungal glycosidases providing important insights towards understanding the aggregation and stability of glycated proteins.
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Affiliation(s)
- Ahana Das
- Department of Microbiology, Maulana Azad College, 8 Rafi Ahmed Kidwai Road, Kolkata 700013, West Bengal, India
| | - Pijush Basak
- Jagadis Bose National Science Talent Search, 1300, Rajdanga Main Road, Sector C, East Kolkata Township, Kolkata 700107, West Bengal, India
| | - Arnab Pramanick
- Jagadis Bose National Science Talent Search, 1300, Rajdanga Main Road, Sector C, East Kolkata Township, Kolkata 700107, West Bengal, India
| | - Rajib Majumder
- School of Life Science and Biotechnology, Department of Biotechnology, Adamas University, Kolkata 700126, West Bengal, India
| | - Debadrita Pal
- Department of Biology, New Mexico State University, PO Box 30001, MSC 3AF, Las Cruces, NM 88003, United States of America
| | - Avishek Ghosh
- Department of Microbiology, Maulana Azad College, 8 Rafi Ahmed Kidwai Road, Kolkata 700013, West Bengal, India
| | - Manas Guria
- Department of Biochemistry, University of Calcutta, 35, Ballygunge Circular Road, Kolkata 700019, West Bengal, India
| | - Maitree Bhattacharyya
- Jagadis Bose National Science Talent Search, 1300, Rajdanga Main Road, Sector C, East Kolkata Township, Kolkata 700107, West Bengal, India.
| | - Samudra Prosad Banik
- Department of Microbiology, Maulana Azad College, 8 Rafi Ahmed Kidwai Road, Kolkata 700013, West Bengal, India.
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19
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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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20
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Sun XB, Lim GT, Lee J, Wan JX, Lin HZ, Yang JM, Wang Q, Park YD. Effects of osmolytes on the refolding of recombinant Pelodiscus sinensis brain-type creatine kinase. Process Biochem 2018. [DOI: 10.1016/j.procbio.2018.02.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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21
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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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22
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Hernández-Meza JM, Sampedro JG. Trehalose Mediated Inhibition of Lactate Dehydrogenase from Rabbit Muscle. The Application of Kramers' Theory in Enzyme Catalysis. J Phys Chem B 2018; 122:4309-4317. [PMID: 29595977 DOI: 10.1021/acs.jpcb.8b01656] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Lactate dehydrogenase (LDH) catalyzes the reduction of pyruvate to lactate by using NADH. LDH kinetics has been proposed to be dependent on the dynamics of a loop over the active site. Kramers' theory has been useful in the study of enzyme catalysis dependent on large structural dynamics. In this work, LDH kinetics was studied in the presence of trehalose and at different temperatures. In the absence of trehalose, temperature increase raised exponentially the LDH Vmax and revealed a sigmoid transition of Km toward a low-affinity state similar to protein unfolding. Notably, LDH Vmax diminished when in the presence of trehalose, while pyruvate affinity increased and the temperature-mediated binding site transition was hindered. The effect of trehalose on kcat was viscosity dependent as described by Kramers' theory since Vmax correlated inversely with the viscosity of the medium. As a result, activation energy ( Ea) for pyruvate reduction was dramatically increased by trehalose presence. This work provides experimental evidence that the dynamics of a structural component in LDH is essential for catalysis, i.e., the closing of the loop on the active site. While the trehalose mediated-increased of pyruvate affinity is proposed to be due to the compaction and/or increase of structural order at the binding site.
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Affiliation(s)
- Juan M Hernández-Meza
- Instituto de Física, Universidad Autónoma de San Luis Potosí , Manuel Nava 6, Zona Universitaria , C.P. 78290 San Luis Potosí , SLP , México
| | - José G Sampedro
- Instituto de Física, Universidad Autónoma de San Luis Potosí , Manuel Nava 6, Zona Universitaria , C.P. 78290 San Luis Potosí , SLP , México
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23
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The opposing effect of urea and high pressure on the conformation of the protein β-hairpin: A molecular dynamics simulation study. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2017.12.054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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24
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Anumalla B, Prabhu NP. Glutamate Induced Thermal Equilibrium Intermediate and Counteracting Effect on Chemical Denaturation of Proteins. J Phys Chem B 2018; 122:1132-1144. [PMID: 29272129 DOI: 10.1021/acs.jpcb.7b10561] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
When organisms are subjected to stress conditions, one of their adaptive responses is accumulation of small organic molecules called osmolytes. These osmolytes affect the structure and stability of the biological macromolecules including proteins. The present study examines the effect of a negatively charged amino acid osmolyte, glutamate (Glu), on two model proteins, ribonuclease A (RNase A) and α-lactalbumin (α-LA), which have positive and negative surface charges at pH 7, respectively. These proteins follow two-state unfolding transitions during both heat and chemical induced denaturation processes. The addition of Glu stabilizes the proteins against temperature and induces an early equilibrium intermediate during unfolding. The stability is found to be enthalpy-driven, and the free energy of stabilization is more for α-LA compared to RNase A. The decrease in the partial molar volume and compressibility of both of the proteins in the presence of Glu suggests that the proteins attain a more compact state through surface hydration which could provide a more stable conformation. This is also supported by molecule dynamic simulation studies which demonstrate that the water density around the proteins is increased upon the addition of Glu. Further, the intermediates could be completely destabilized by lower concentrations (∼0.5 M) of guanidinium chloride and salt. However, urea subverts the Glu-induced intermediate formed by α-LA, whereas it only slightly destabilizes in the case of RNase A which has a positive surface charge and could possess charge-charge interactions with Glu. This suggests that, apart from hydration, columbic interactions might also contribute to the stability of the intermediate. Gdm-induced denaturation of RNase A and α-LA in the absence and the presence of Glu at different temperatures was carried out. These results also show the Glu-induced stabilization of both of the proteins; however, all of the unfolding transitions followed two-state transitions during chemical denaturation. The extent of stability exerted by Glu is higher for RNase A at higher temperature, whereas it provides more stability for α-LA at lower temperature. Thus, the experiments indicate that Glu induces a thermal equilibrium intermediate and increases the thermodynamic stability of proteins irrespective of their surface charges. The extent of stability varies between the proteins in a temperature-dependent manner.
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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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25
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Rani A, Venkatesu P. Changing relations between proteins and osmolytes: a choice of nature. Phys Chem Chem Phys 2018; 20:20315-20333. [DOI: 10.1039/c8cp02949k] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The stabilization and destabilization of the protein in the presence of any additive is mainly attributed to its preferential exclusion from protein surface and its preferential binding to the protein surface, respectively.
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Affiliation(s)
- Anjeeta Rani
- Department of Chemistry
- University of Delhi
- Delhi 110 007
- India
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26
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Das A, Basak P, Pattanayak R, Kar T, Majumder R, Pal D, Bhattacharya A, Bhattacharyya M, Banik SP. Trehalose induced structural modulation of Bovine Serum Albumin at ambient temperature. Int J Biol Macromol 2017; 105:645-655. [DOI: 10.1016/j.ijbiomac.2017.07.074] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/07/2017] [Accepted: 07/12/2017] [Indexed: 10/19/2022]
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27
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Das S, Paul S. Hydrotropic Solubilization of Sparingly Soluble Riboflavin Drug Molecule in Aqueous Nicotinamide Solution. J Phys Chem B 2017; 121:8774-8785. [DOI: 10.1021/acs.jpcb.7b05774] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shubhadip Das
- Department of Chemistry, Indian Institute of Technology, Guwahati,Assam 781039, India
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati,Assam 781039, India
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28
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Yahyaei M, Mehrnejad F, Naderi-manesh H, Rezayan AH. Follicle-stimulating hormone encapsulation in the cholesterol-modified chitosan nanoparticles via molecular dynamics simulations and binding free energy calculations. Eur J Pharm Sci 2017; 107:126-137. [DOI: 10.1016/j.ejps.2017.07.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 06/02/2017] [Accepted: 07/07/2017] [Indexed: 12/17/2022]
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29
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Yamamori Y, Matubayasi N. Interaction-component analysis of the effects of urea and its alkylated derivatives on the structure of T4-lysozyme. J Chem Phys 2017; 146:225103. [DOI: 10.1063/1.4985222] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Yu Yamamori
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
- Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Katsura, Kyoto 615-8520, Japan
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30
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Das S, Paul S. Hydrotropic Action of Cationic Hydrotrope p-Toluidinium Chloride on the Solubility of Sparingly Soluble Gliclazide Drug Molecule: A Computational Study. J Chem Inf Model 2017; 57:1461-1473. [DOI: 10.1021/acs.jcim.7b00182] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shubhadip Das
- 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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31
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32
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Murakami S, Hayashi T, Kinoshita M. Effects of salt or cosolvent addition on solubility of a hydrophobic solute in water: Relevance to those on thermal stability of a protein. J Chem Phys 2017; 146:055102. [DOI: 10.1063/1.4975165] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [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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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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34
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Borgohain G, Mandal B, Paul S. Molecular dynamics approach to understand the denaturing effect of a millimolar concentration of dodine on a λ-repressor and counteraction by trehalose. Phys Chem Chem Phys 2017; 19:13160-13171. [DOI: 10.1039/c6cp08289k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Here, we use a molecular dynamics approach to calculate the spatial distribution function of the ternary water–dodine–trehalose (1.0 M) system.
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Affiliation(s)
- Gargi Borgohain
- Department of Chemistry
- Indian Institute of Technology
- Guwahati
- India
| | | | - Sandip Paul
- Department of Chemistry
- Indian Institute of Technology
- Guwahati
- India
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35
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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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36
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Zhao L, Pan L, Cao Z, Wang Q. Mutual Effects of Glycerol and Inorganic Salts on Their Hydration Abilities. J Phys Chem B 2016; 120:13112-13117. [DOI: 10.1021/acs.jpcb.6b08778] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lishan Zhao
- Department
of Physics, University of Science and Technology Beijing, Beijing 100083, China
- Institute
of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Liqing Pan
- Department
of Physics, University of Science and Technology Beijing, Beijing 100083, China
| | - Zexian Cao
- Institute
of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Qiang Wang
- Institute
of Physics, Chinese Academy of Sciences, Beijing 100190, China
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37
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Lindsay RJ, Johnson QR, Evangelista W, Nellas RB, Shen T. DMSO enhanced conformational switch of an interfacial enzyme. Biopolymers 2016; 105:864-72. [PMID: 27463323 DOI: 10.1002/bip.22924] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 07/25/2016] [Indexed: 11/05/2022]
Abstract
Interfacial proteins function in unique heterogeneous solvent environments, such as water-oil interfaces. One important example is microbial lipase, which is activated in an oil-water emulsion phase and has many important enzymatic functions. A unique aprotic dipolar organic solvent, dimethyl sulfoxide (DMSO), has been shown to increase the activity of lipases, but the mechanism behind this enhancement is still unknown. Here, all-atom molecular dynamics simulations of lipase in a binary solution were performed to examine the effects of DMSO on the dynamics of the gating mechanism. The amphiphilic α5 region of the lipase was a focal point for the analysis, since the structural ordering of α5 has been shown to be important for gating under other perturbations. Compared to the closed-gorge ensemble in an aqueous environment, the conformational ensemble shifts towards open-gorge structures in the presence of DMSO solvents. Increased width of the access channel is particularly prevalent in 45% and 60% DMSO concentrations (w/w). As the amount of DMSO increases, the α5 region of the lipase becomes more α-helical, as we previously observed in studies that address water-oil interfacial and high pressure activation. We believe that the structural ordering of α5 plays an essential role on gating and lipase activity.
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Affiliation(s)
- Richard J Lindsay
- UT-ORNL Graduate School of Genome Science and Technology, Knoxville, TN, 37996.,Oak Ridge National Laboratory, Center for Molecular Biophysics, Oak Ridge, TN, 37830
| | - Quentin R Johnson
- Oak Ridge National Laboratory, Center for Molecular Biophysics, Oak Ridge, TN, 37830.,National Institute for Mathematical and Biological Synthesis, Knoxville, TN, 37996
| | - Wilfredo Evangelista
- Oak Ridge National Laboratory, Center for Molecular Biophysics, Oak Ridge, TN, 37830.,Department of Biochemistry and Cellular & Molecular Biology, University of Tennessee, Knoxville, TN, 37996
| | - Ricky B Nellas
- Institute of Chemistry, University of the Philippines Diliman, Quezon City, Philippines
| | - Tongye Shen
- Oak Ridge National Laboratory, Center for Molecular Biophysics, Oak Ridge, TN, 37830. .,Department of Biochemistry and Cellular & Molecular Biology, University of Tennessee, Knoxville, TN, 37996.
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38
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Spinozzi F, Mariani P, Ortore MG. Proteins in binary solvents. Biophys Rev 2016; 8:87-106. [PMID: 28510051 PMCID: PMC5425779 DOI: 10.1007/s12551-016-0193-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 02/01/2016] [Indexed: 01/09/2023] Open
Abstract
Proteins in living organisms exist in complex aqueous solutions or embedded in membranes. In solution, proteins are surrounded by a tightly bound hydration layer, which is more ordered and less mobile than bulk water. As a consequence, water plays a major role in controlling protein structure stability, conformational flexibility, dynamics, and functionality, but it also appears that protein surface regulates the structuring of the surrounding water. The presence of cosolvents can modify the hydration layer characteristics and then the whole protein structural and dynamical properties. Because cytoplasm or biological liquids are complex solutions, the knowledge of the solvation shell characteristics in mixed solvents should be considered as a crucial step in describing biological processes at molecular level. This review reports on recent studies on the structural and thermodynamic properties of model proteins dissolved in binary solvent mixtures by small-angle neutron scattering (SANS) and differential scanning microcalorimetry (DSC) techniques. We will show that contrast variation SANS experiments allow to acquire a direct knowledge of both protein structure and protein solvation shell (in terms of low-resolution shape and solvent/cosolvent composition), while DSC experiments provide information on all the relevant thermodynamic properties. We will focus on two main points. First, an extended description of the thermodynamic model used to define the equilibria between water and cosolvent molecules in the protein solvation shell will be presented. Second, the determination of the peculiar characteristics of the protein solvation layer, which will be illustrated by considering different systems. As a conclusion, we will show that the investigation of structure and thermodynamics of proteins in binary aqueous mixtures is an important way to understand the role of hydration in protein stability and activity.
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Affiliation(s)
- Francesco Spinozzi
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy.
| | - Paolo Mariani
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Maria Grazia Ortore
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
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39
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Das S, Paul S. Computer Simulation Studies of the Mechanism of Hydrotrope-Assisted Solubilization of a Sparingly Soluble Drug Molecule. J Phys Chem B 2016; 120:3540-50. [DOI: 10.1021/acs.jpcb.5b11902] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shubhadip Das
- Department
of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India
| | - Sandip Paul
- Department
of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India
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40
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Yang X, Jiang L, Jia Y, Hu Y, Xu Q, Xu X, Huang H. Counteraction of Trehalose on N, N-Dimethylformamide-Induced Candida rugosa Lipase Denaturation: Spectroscopic Insight and Molecular Dynamic Simulation. PLoS One 2016; 11:e0152275. [PMID: 27031946 PMCID: PMC4816565 DOI: 10.1371/journal.pone.0152275] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 03/12/2016] [Indexed: 11/18/2022] Open
Abstract
Candida rugosa lipase (CRL) has been widely used as a biocatalyst for non-aqueous synthesis in biotechnological applications, which, however, often suffers significant loss of activity in organic solvent. Experimental results show that trehalose could actively counteract the organic-solvent-induced protein denaturation, while the molecular mechanisms still don’t unclear. Herein, CRL was used as a model enzyme to explore the effects of trehalose on the retention of enzymatic activity upon incubation in N,N-dimethylformamide (DMF). Results showed that both catalytic activity and conformation changes of CRL influenced by DMF solvent were inhibited by trehalose in a dose-dependent fashion. The simulations further indicated that the CRL protein unfolded in binary DMF solution, but retained the native state in the ternary DMF/trehalose system. Trehalose as the second osmolyte added into binary DMF solution decreased DMF-CRL hydrogen bonds efficiently, whereas increased the intermolecular hydrogen bondings between DMF and trehalose. Thus, the origin of its denaturing effects of DMF on protein is thought to be due to the preferential exclusion of trehalose as well as the intermolecular hydrogen bondings between trehalose and DMF. These findings suggest that trehalose protect the CRL protein from DMF-induced unfolding via both indirect and direct interactions.
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Affiliation(s)
- Xin Yang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 210009, PR China
| | - Ling Jiang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 210009, PR China
- * E-mail: (LJ); (HH)
| | - Yigang Jia
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 210009, PR China
| | - Yi Hu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 210009, PR China
| | - Qing Xu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 210009, PR China
| | - Xian Xu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 210009, PR China
| | - He Huang
- College of Pharmaceutical Sciences, Nanjing Tech University, Nanjing 210009, PR China
- * E-mail: (LJ); (HH)
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Murakami S, Kinoshita M. Effects of monohydric alcohols and polyols on the thermal stability of a protein. J Chem Phys 2016; 144:125105. [PMID: 27036482 DOI: 10.1063/1.4944680] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The thermal stability of a protein is lowered by the addition of a monohydric alcohol, and this effect becomes larger as the size of hydrophobic group in an alcohol molecule increases. By contrast, it is enhanced by the addition of a polyol possessing two or more hydroxyl groups per molecule, and this effect becomes larger as the number of hydroxyl groups increases. Here, we show that all of these experimental observations can be reproduced even in a quantitative sense by rigid-body models focused on the entropic effect originating from the translational displacement of solvent molecules. The solvent is either pure water or water-cosolvent solution. Three monohydric alcohols and five polyols are considered as cosolvents. In the rigid-body models, a protein is a fused hard spheres accounting for the polyatomic structure in the atomic detail, and the solvent is formed by hard spheres or a binary mixture of hard spheres with different diameters. The effective diameter of cosolvent molecules and the packing fractions of water and cosolvent, which are crucially important parameters, are carefully estimated using the experimental data of properties such as the density of solid crystal of cosolvent, parameters in the pertinent cosolvent-cosolvent interaction potential, and density of water-cosolvent solution. We employ the morphometric approach combined with the integral equation theory, which is best suited to the physical interpretation of the calculation result. It is argued that the degree of solvent crowding in the bulk is the key factor. When it is made more serious by the cosolvent addition, the solvent-entropy gain upon protein folding is magnified, leading to the enhanced thermal stability. When it is made less serious, the opposite is true. The mechanism of the effects of monohydric alcohols and polyols is physically the same as that of sugars. However, when the rigid-body models are employed for the effect of urea, its addition is predicted to enhance the thermal stability, which conflicts with the experimental fact. We then propose, as two essential factors, not only the solvent-entropy gain but also the loss of protein-solvent interaction energy upon protein folding. The competition of changes in these two factors induced by the cosolvent addition determines the thermal-stability change.
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Affiliation(s)
- Shota Murakami
- Graduate School of Energy Science, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Masahiro Kinoshita
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
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Borgohain G, Paul S. Model Dependency of TMAO’s Counteracting Effect Against Action of Urea: Kast Model versus Osmotic Model of TMAO. J Phys Chem B 2016; 120:2352-61. [DOI: 10.1021/acs.jpcb.5b10968] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gargi Borgohain
- Department of Chemistry, Indian Institute of Technology, Guwahati 781039, India
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati 781039, India
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