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Ghosh S, Prabhu NP. Heterogeneous Macromolecular crowding effect on nucleation-independent fibril formation of Lysozyme: Spectroscopic analysis of Structure, Stability, and fibrillation rate. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 315:124276. [PMID: 38626673 DOI: 10.1016/j.saa.2024.124276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 04/05/2024] [Accepted: 04/09/2024] [Indexed: 04/18/2024]
Affiliation(s)
- Subhasree Ghosh
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - N Prakash Prabhu
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India.
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2
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Lampitella EA, Marone M, Achanta NSK, Porzio E, Trepiccione F, Manco G. The Human Paraoxonase 2: An Optimized Procedure for Refolding and Stabilization Facilitates Enzyme Analyses and a Proteomics Approach. Molecules 2024; 29:2434. [PMID: 38893310 PMCID: PMC11173892 DOI: 10.3390/molecules29112434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 05/16/2024] [Accepted: 05/20/2024] [Indexed: 06/21/2024] Open
Abstract
The human paraoxonase 2 (PON2) is the oldest member of a small family of arylesterase and lactonase enzymes, representing the first line of defense against bacterial infections and having a major role in ROS-associated diseases such as cancer, cardiovascular diseases, neurodegeneration, and diabetes. Specific Post-Translational Modifications (PTMs) clustering nearby two residues corresponding to pon2 polymorphic sites and their impact on the catalytic activity are not yet fully understood. Thus, the goal of the present study was to develop an improved PON2 purification protocol to obtain a higher amount of protein suitable for in-depth biochemical studies and biotechnological applications. To this end, we also tested several compounds to stabilize the active monomeric form of the enzyme. Storing the enzyme at 4 °C with 30 mM Threalose had the best impact on the activity, which was preserved for at least 30 days. The catalytic parameters against the substrate 3-Oxo-dodecanoyl-Homoserine Lactone (3oxoC12-HSL) and the enzyme ability to interfere with the biofilm formation of Pseudomonas aeruginosa (PAO1) were determined, showing that the obtained enzyme is well suited for downstream applications. Finally, we used the purified rPON2 to detect, by the direct molecular fishing (DMF) method, new putative PON2 interactors from soluble extracts of HeLa cells.
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Affiliation(s)
- Eros A. Lampitella
- Institute of Biochemistry and Cell Biology-CNR, Via Pietro Castellino 111, 80131 Naples, Italy; (E.A.L.); (M.M.); (N.S.K.A.); (E.P.)
| | - Maria Marone
- Institute of Biochemistry and Cell Biology-CNR, Via Pietro Castellino 111, 80131 Naples, Italy; (E.A.L.); (M.M.); (N.S.K.A.); (E.P.)
| | - Nagendra S. K. Achanta
- Institute of Biochemistry and Cell Biology-CNR, Via Pietro Castellino 111, 80131 Naples, Italy; (E.A.L.); (M.M.); (N.S.K.A.); (E.P.)
| | - Elena Porzio
- Institute of Biochemistry and Cell Biology-CNR, Via Pietro Castellino 111, 80131 Naples, Italy; (E.A.L.); (M.M.); (N.S.K.A.); (E.P.)
| | - Francesco Trepiccione
- Department of Translational Medical Science, University of Campania “Luigi Vanvitelli”, Via Leonardo Bianchi c/o Ospedale Monaldi, 80131 Naples, Italy;
| | - Giuseppe Manco
- Institute of Biochemistry and Cell Biology-CNR, Via Pietro Castellino 111, 80131 Naples, Italy; (E.A.L.); (M.M.); (N.S.K.A.); (E.P.)
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Lisitsa AE, Sukovatyi LA, Deeva AA, Gulnov DV, Esimbekova EN, Kratasyuk VA, Nemtseva EV. The Role of Cosolvent-Water Interactions in Effects of the Media on Functionality of Enzymes: A Case Study of Photobacterium leiognathi Luciferase. Life (Basel) 2023; 13:1384. [PMID: 37374166 DOI: 10.3390/life13061384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 06/08/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
A complex heterogeneous intracellular environment seems to affect enzymatic catalysis by changing the mobility of biomolecules, their stability, and their conformational states, as well as by facilitating or hindering continuously occurring interactions. The evaluation and description of the influence of the cytoplasmic matrix components on enzymatic activity are problems that remain unsolved. In this work, we aimed to determine the mechanisms of action of two-component media with cosolvents of various molecular sizes on the complex multi-stage bioluminescent reaction catalyzed by bacterial luciferase. Kinetic and structural effects of ethylene glycol, glycerol, sorbitol, glucose, sucrose, dextran, and polyethylene glycol on bacterial luciferase were studied using stopped-flow and fluorescence spectroscopy techniques and molecular dynamics simulations. We have found that diffusion limitations in the presence of cosolvents promote the stabilization of flavin substrate and peroxyflavin intermediate of the reaction, but do not provide any advantages in bioluminescence quantum yield, because substrate binding is slowed down as well. The catalytic constant of bacterial luciferase has been found to be viscosity-independent and correlated with parameters of water-cosolvent interactions (Norrish constant, van der Waals interaction energies). Crowding agents, in contrast to low-molecular-weight cosolvents, had little effect on peroxyflavin intermediate decay and enzyme catalytic constant. We attributed specific kinetic effects to the preferential interaction of the cosolvents with enzyme surface and their penetration into the active site.
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Affiliation(s)
- Albert E Lisitsa
- Biophysics Department, Siberian Federal University, 660041 Krasnoyarsk, Russia
| | - Lev A Sukovatyi
- Biophysics Department, Siberian Federal University, 660041 Krasnoyarsk, Russia
| | - Anna A Deeva
- Biophysics Department, Siberian Federal University, 660041 Krasnoyarsk, Russia
| | - Dmitry V Gulnov
- Biophysics Department, Siberian Federal University, 660041 Krasnoyarsk, Russia
| | - Elena N Esimbekova
- Biophysics Department, Siberian Federal University, 660041 Krasnoyarsk, Russia
- Institute of Biophysics, Siberian Branch of Russian Academy of Sciences, 660036 Krasnoyarsk, Russia
| | - Valentina A Kratasyuk
- Biophysics Department, Siberian Federal University, 660041 Krasnoyarsk, Russia
- Institute of Biophysics, Siberian Branch of Russian Academy of Sciences, 660036 Krasnoyarsk, Russia
| | - Elena V Nemtseva
- Biophysics Department, Siberian Federal University, 660041 Krasnoyarsk, Russia
- Institute of Biophysics, Siberian Branch of Russian Academy of Sciences, 660036 Krasnoyarsk, Russia
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4
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Chu IT, Hutcheson BO, Malsch HR, Pielak GJ. Macromolecular Crowding by Polyethylene Glycol Reduces Protein Breathing. J Phys Chem Lett 2023; 14:2599-2605. [PMID: 36881386 DOI: 10.1021/acs.jpclett.3c00271] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Most efforts to understand macromolecular crowding focus on global (i.e., complete) unfolding, but smaller excursions, often called breathing, promote aggregation, which is associated with several diseases and the bane of pharmaceutical and commercial protein production. We used NMR to assess the effects of ethylene glycol (EG) and polyethylene glycols (PEGs) on the structure and stability of the B1 domain of protein G (GB1). Our data show that EG and PEGs stabilize GB1 differently. EG interacts with GB1 more strongly than PEGs, but neither affects the structure of the folded state. EG and 12000 g/mol PEG stabilize GB1 more than PEGs of intermediate size, but EG and smaller PEGs stabilize GB1 enthalpically while the largest PEG acts entropically. Our key finding is that PEGs turn local unfolding into global unfolding, and meta-analysis of published data supports this conclusion. These efforts provide knowledge that can be applied to improve biological drugs and commercial enzymes.
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Affiliation(s)
- I-Te Chu
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Brent O Hutcheson
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Hudson R Malsch
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Gary J Pielak
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
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5
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Stewart CJ, Olgenblum GI, Propst A, Harries D, Pielak GJ. Resolving the enthalpy of protein stabilization by macromolecular crowding. Protein Sci 2023; 32:e4573. [PMID: 36691735 PMCID: PMC9942490 DOI: 10.1002/pro.4573] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 01/11/2023] [Accepted: 01/13/2023] [Indexed: 01/25/2023]
Abstract
Proteins in the cellular milieu reside in environments crowded by macromolecules and other solutes. Although crowding can significantly impact the protein folded state stability, most experiments are conducted in dilute buffered solutions. To resolve the effect of crowding on protein stability, we use 19 F nuclear magnetic resonance spectroscopy to follow the reversible, two-state unfolding thermodynamics of the N-terminal Src homology 3 domain of the Drosophila signal transduction protein drk in the presence of polyethylene glycols (PEGs) of various molecular weights and concentrations. Contrary to most current theories of crowding that emphasize steric protein-crowder interactions as the main driving force for entropically favored stabilization, our experiments show that PEG stabilization is accompanied by significant heat release, and entropy disfavors folding. Using our newly developed model, we find that stabilization by ethylene glycol and small PEGs is driven by favorable binding to the folded state. In contrast, for larger PEGs, chemical or soft PEG-protein interactions do not play a significant role. Instead, folding is favored by excluded volume PEG-protein interactions and an exothermic nonideal mixing contribution from release of confined PEG and water upon folding. Our results indicate that crowding acts through molecular interactions subtler than previously assumed and that interactions between solution components with both the folded and unfolded states must be carefully considered.
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Affiliation(s)
- Claire J. Stewart
- Department of ChemistryUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Gil I. Olgenblum
- Institute of Chemistry & the Fritz Haber Research Center, The Hebrew UniversityJerusalemIsrael
| | - Ashlee Propst
- Department of ChemistryUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Daniel Harries
- Institute of Chemistry & the Fritz Haber Research Center, The Hebrew UniversityJerusalemIsrael
| | - Gary J. Pielak
- Department of ChemistryUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
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Terukina T, Tanaka J, Takayama Y, Osanai K, Kino S, Kanazawa T, Kondo H. Sangelose-based gels and films: effects of glycerol and α-cyclodextrin and their pharmaceutical application. Drug Dev Ind Pharm 2023; 49:75-83. [PMID: 36803493 DOI: 10.1080/03639045.2023.2182127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
OBJECTIVE To evaluate the possible application of Sangelose as an alternative to gelatin and carrageenan for the development of film substrates, and to examine the effect of glycerol and α-cyclodextrin (α-CyD) on the viscoelastic properties of Sangelose-based gels and the physical properties of the films. SIGNIFICANCE Sangelose-based gels/films can serve as a potential viable alternative to gelatin and carrageenan in pharmaceutical applications. METHODS Glycerol (a plasticizer) and α-CyD (a functional additive) were added to Sangelose, and gels and films were prepared. The gels were evaluated by dynamic viscoelasticity measurements, and the films were evaluated by scanning electron microscopy, Fourier-transform infrared spectroscopy, tensile tests, and contact angle measurements. Soft capsules were prepared using the formulated gels. RESULTS The strength of the gels was affected when only glycerol was added to Sangelose and α-CyD addition resulted in rigid gels. However, the addition of α-CyD with 10% glycerol weakened the gels. Tensile tests suggested that glycerol addition affected the formability and malleability of the films, while α-CyD addition affected their formability and elongation properties. The addition of 10% glycerol and α-CyD did not affect the flexibility of the films, suggesting that the malleability and strength were impacted. Soft capsules could not be prepared by adding only glycerol or α-CyD to Sangelose. Soft capsules with favorable disintegration behavior were obtained upon adding α-CyD to gels along with 10% glycerol. CONCLUSIONS Sangelose combined with a suitable amount of glycerol and α-CyD has preferable characteristics for film formation and may have potential applications in the pharmaceutical and health food sectors.
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Affiliation(s)
- Takayuki Terukina
- Department of Pharmaceutical Engineering and Drug Delivery Sciences, Graduate School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Jun Tanaka
- Department of Pharmaceutical Engineering and Drug Delivery Sciences, Graduate School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Yumi Takayama
- Department of Pharmaceutical Engineering and Drug Delivery Sciences, Graduate School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Kaede Osanai
- Department of Pharmaceutical Engineering and Drug Delivery Sciences, Graduate School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Shusuke Kino
- Department of Pharmaceutical Engineering and Drug Delivery Sciences, Graduate School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Takanori Kanazawa
- Department of Pharmaceutical Engineering and Drug Delivery Sciences, Graduate School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Hiromu Kondo
- Department of Pharmaceutical Engineering and Drug Delivery Sciences, Graduate School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
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Naidu KT, Prabhu NP. Polyols, increasing global stability of cytochrome c, destabilize the thermal unfolding intermediate. J Biomol Struct Dyn 2022; 40:11216-11228. [PMID: 34308796 DOI: 10.1080/07391102.2021.1956593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Studies on the intermediate states of proteins provide essential information on folding pathway and energy landscape of proteins. Osmolytes, known to alter the stability of proteins, might also affect the structure and energy states of folding intermediates. This was examined using cytochrome c (Cyt) as a model protein which forms a spectroscopically detectable intermediate during thermal denaturation transition. Most of the secondary structure and the native heme-ligation were intact in the intermediate state of the protein. Denaturants, urea and guanidinium hydrochloride, and ionic salt destabilizes the intermediate and drive the protein to follow two-state transition. The effect of polyol class of osmolytes, glycol, glycerol, erythritol, xylitol and sorbitol (with OH-groups two to six), on the intermediate was studied using Soret absorbance and far-UV circular dichroism. With the increasing concentration of any of the polyols, the transition-midpoint temperature (Tm) and the enthalpy change (ΔH) for native to intermediate transition were decreased. This indicated that the intermediate was destabilized by the polyols. However, the polyols increased the overall stability of the protein by increasing Tm and ΔH for intermediate to unfolded transition, except for glycol which destabilized the protein. These results show that the polyols could alter the energy state of the intermediate, and the effect of lower and higher polyols might be different on the stability and folding pathway of the protein.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- K Tejaswi Naidu
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - N Prakash Prabhu
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India
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8
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Kawai F, Furushima Y, Mochizuki N, Muraki N, Yamashita M, Iida A, Mamoto R, Tosha T, Iizuka R, Kitajima S. Efficient depolymerization of polyethylene terephthalate (PET) and polyethylene furanoate by engineered PET hydrolase Cut190. AMB Express 2022; 12:134. [DOI: 10.1186/s13568-022-01474-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 10/05/2022] [Indexed: 11/10/2022] Open
Abstract
AbstractThe enzymatic recycling of polyethylene terephthalate (PET) can be a promising approach to tackle the problem of plastic waste. The thermostability and activity of PET-hydrolyzing enzymes are still insufficient for practical application. Pretreatment of PET waste is needed for bio-recycling. Here, we analyzed the degradation of PET films, packages, and bottles using the newly engineered cutinase Cut190. Using gel permeation chromatography and high-performance liquid chromatography, the degradation of PET films by the Cut190 variant was shown to proceed via a repeating two-step hydrolysis process; initial endo-type scission of a surface polymer chain, followed by exo-type hydrolysis to produce mono/bis(2-hydroxyethyl) terephthalate and terephthalate from the ends of fragmented polymer molecules. Amorphous PET powders were degraded more than twofold higher than amorphous PET film with the same weight. Moreover, homogenization of post-consumer PET products, such as packages and bottles, increased their degradability, indicating the importance of surface area for the enzymatic hydrolysis of PET. In addition, it was required to maintain an alkaline pH to enable continuous enzymatic hydrolysis, by increasing the buffer concentration (HEPES, pH 9.0) depending on the level of the acidic products formed. The cationic surfactant dodecyltrimethylammonium chloride promoted PET degradation via adsorption on the PET surface and binding to the anionic surface of the Cut190 variant. The Cut190 variant also hydrolyzed polyethylene furanoate. Using the best performing Cut190 variant (L136F/Q138A/S226P/R228S/D250C-E296C/Q123H/N202H/K305del/L306del/N307del) and amorphous PET powders, more than 90 mM degradation products were obtained in 3 days and approximately 80 mM in 1 day.
Graphical Abstract
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9
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Ballauff M. Denaturation of proteins: electrostatic effects vs. hydration. RSC Adv 2022; 12:10105-10113. [PMID: 35424951 PMCID: PMC8968186 DOI: 10.1039/d2ra01167k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 03/23/2022] [Indexed: 11/25/2022] Open
Abstract
The unfolding transition of proteins in aqueous solution containing various salts or uncharged solutes is a classical subject of biophysics. In many cases, this transition is a well-defined two-stage equilibrium process which can be described by a free energy of transition ΔGu and a transition temperature Tm. For a long time, it has been known that solutes can change Tm profoundly. Here we present a phenomenological model that describes the change of Tm with the solute concentration cs in terms of two effects: (i) the change of the number of correlated counterions Δnci and (ii) the change of hydration expressed through the parameter Δw and its dependence on temperature expressed through the parameter dΔcp/dcs. Proteins always carry charges and Δnci describes the uptake or release of counterions during the transition. Likewise, the parameter Δw measures the uptake or release of water during the transition. The transition takes place in a reservoir with a given salt concentration cs that defines also the activity of water. The parameter Δnci is a measure for the gain or loss of free energy because of the release or uptake of ions and is related to purely entropic effects that scale with ln cs. Δw describes the effect on ΔGu through the loss or uptake of water molecules and contains enthalpic as well as entropic effects that scale with cs. It is related to the enthalpy of transition ΔHu through a Maxwell relation: the dependence of ΔHu on cs is proportional to the dependence of Δw on temperature. While ionic effects embodied in Δnci are independent of the kind of salt, the hydration effects described through Δw are directly related to Hofmeister effects of the various salt ions. A comparison with literature data underscores the general validity of the model. A phenomenological approach to the unfolding transition of proteins is given. The model treats quantitatively the effect of electrostatics as well as of hydration (Hofmeister effects).![]()
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Affiliation(s)
- Matthias Ballauff
- Institut für Chemie und Biochemie, Freie Universität Berlin Takustraße 3 14195 Berlin Germany
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Kushwaha P, Prabhu NP. Imidazolium-based ionic liquids with increasing alkyl chain length of cations decrease the stability and fibrillation propensity of lysozyme. NEW J CHEM 2022. [DOI: 10.1039/d2nj00559j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Imidazolium ionic liquids with longer alkyl side chains show a larger destabilization effect on lysozyme. Increased hydrophobicity of the IL increases its binding affinity and inhibits the fibril formation of lysozyme.
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Affiliation(s)
- Pratibha Kushwaha
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad – 500 046, India
| | - N. Prakash Prabhu
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad – 500 046, India
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11
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Ou X, Lao Y, Xu J, Wutthinitikornkit Y, Shi R, Chen X, Li J. ATP Can Efficiently Stabilize Protein through a Unique Mechanism. JACS AU 2021; 1:1766-1777. [PMID: 34723279 PMCID: PMC8549052 DOI: 10.1021/jacsau.1c00316] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Indexed: 06/13/2023]
Abstract
Recent experiments suggested that ATP can effectively stabilize protein structure and inhibit protein aggregation when its concentration is less than 10 mM, which is significantly lower than cosolvent concentrations required in conventional mechanisms. The ultrahigh efficiency of ATP suggests a unique mechanism that is fundamentally different from previous models of cosolvents. In this work, we used molecular dynamics simulation and experiments to study the interactions of ATPs with three proteins: lysozyme, ubiquitin, and malate dehydrogenase. ATP tends to bind to the surface regions with high flexibility and high degree of hydration. These regions are also vulnerable to thermal perturbations. The bound ATPs further assemble into ATP clusters mediated by Mg2+ and Na+ ions. More interestingly, in Mg2+-free ATP solution, Na+ at higher concentration (150 mM under physiological conditions) can similarly mediate the formation of the ATP cluster on protein. The ATP cluster can effectively reduce the fluctuations of the vulnerable region and thus stabilize the protein against thermal perturbations. Both ATP binding and the considerable improvement of thermal stability of ATP-bound protein were verified by experiments.
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Affiliation(s)
- Xinwen Ou
- Zhejiang
Province Key Laboratory of Quantum Technology and Device, Department
of Physics, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
| | - Yichong Lao
- Zhejiang
Province Key Laboratory of Quantum Technology and Device, Department
of Physics, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
| | - Jingjie Xu
- Eye
Center of the Second Affiliated Hospital, Institute of Translational
Medicine, School of Medicine, Zhejiang University, Hangzhou 310009, China
| | - Yanee Wutthinitikornkit
- Zhejiang
Province Key Laboratory of Quantum Technology and Device, Department
of Physics, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
| | - Rui Shi
- Zhejiang
Province Key Laboratory of Quantum Technology and Device, Department
of Physics, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
| | - Xiangjun Chen
- Eye
Center of the Second Affiliated Hospital, Institute of Translational
Medicine, School of Medicine, Zhejiang University, Hangzhou 310009, China
| | - Jingyuan Li
- Zhejiang
Province Key Laboratory of Quantum Technology and Device, Department
of Physics, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
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Affiliation(s)
- Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
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