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Nanavare P, Sarkar S, Jena AB, Chakrabarti R. Osmolyte-induced conformational stabilization of a hydrophobic polymer. Phys Chem Chem Phys 2024; 26:24021-24040. [PMID: 39247939 DOI: 10.1039/d4cp01694g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/10/2024]
Abstract
Elucidating the mechanistic role of osmolytes on conformations of hydrophobic prototypical macromolecules in principle is the stepping stone towards understanding the effect of osmolytes on proteins. Motivated by this, we use equilibrium simulations and umbrella sampling techniques to dissect the underlying mechanism of osmolyte-induced conformational stability of a hydrophobic polymer. Our results unveil a remarkable osmolyte-dependent conformational stabilization of the polymer. In an aqueous solution of 4 M choline chloride (ChCl), the polymer has an even more compact structure than in water. On the other hand, an aqueous solution of 8 M urea stabilizes the extended state of the polymer. Interestingly, the polymer adopts an intermediate hairpin conformation in a mixed osmolyte solution of 4 M ChCl and 8 M urea in water due to the interplay of ChCl and urea. Our simulations identify the relative accumulation of water and the hydrophilic part of choline or preferential binding of urea near the collapsed and the extended states, respectively. Analyses split out the enthalpic and entropic contributions to the overall free energy. This decides the stabilization of the preferred conformation in the chosen osmolyte solution. Our simulations show that in an aqueous solution of ChCl, the hairpin state is stabilized by entropy gain. In contrast, the enthalpic contribution stabilizes the hairpin state in mixed environments. However, a collapsed state is energetically not favored in the presence of urea. In brief, via employing an in silico approach, the current findings indicate the importance of osmolytes in stabilizing the conformational states of hydrophobic polymers.
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Affiliation(s)
- Pooja Nanavare
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India.
| | - Soham Sarkar
- Eduard-Zintl-Institute für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Strasse 8, 64287 Darmstadt, Germany
| | - Abhijit Bijay Jena
- 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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2
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Devi S, Garg DK, Bhat R. Kinetic control in amyloid polymorphism: Different agitation and solution conditions promote distinct amyloid polymorphs of alpha-synuclein. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140917. [PMID: 37061153 DOI: 10.1016/j.bbapap.2023.140917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 04/01/2023] [Accepted: 04/11/2023] [Indexed: 04/17/2023]
Abstract
Aggregation of neuronal protein α-synuclein is implicated in synucleinopathies, including Parkinson's disease. Despite abundant in vitro studies, the mechanism of α-synuclein assembly process remains ambiguous. In this work, α-synuclein aggregation was induced by its constant mixing in two separate modes, either by agitation in a 96-well microplate reader (MP) or in microcentrifuge tubes using a shaker incubator (SI). Aggregation in both modes occurred through a sigmoidal growth pattern with a well-defined lag, growth, and saturation phase. The end-stage MP- and SI-derived aggregates displayed distinct differences in morphological, biochemical, and spectral signatures as discerned through AFM, proteinase-K digestion, FTIR, Raman, and CD spectroscopy. The MP-derived aggregates showed irregular morphology with a significant random coil conformation, contrary to SI-derived aggregates, which showed typical β-sheet fibrillar structures. The end-stage MP aggregates convert to β-rich SI-like aggregates upon 1) seeding with SI-derived aggregates and 2) agitating in SI. We conclude that end-stage MP aggregates were in a kinetically trapped conformation, whose kinetic barrier was bypassed upon either seeding by SI-derived fibrils or shaking in SI. We further show that MP-derived aggregates that form in the presence of sorbitol, an osmolyte, displayed a β-rich signature, indicating that the preferential exclusion effect of osmolytes helped overcome the kinetic barrier. Our findings help in unravelling the kinetic origin of different α-synuclein aggregated polymorphs (strains) that encode diverse variants of synucleinopathies. We demonstrate that kinetic control shapes the polymorphic landscape of α-synuclein aggregates, both through de novo generation of polymorphs, and by their interconversion.
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Affiliation(s)
- Santosh Devi
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Dushyant Kumar Garg
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Rajiv Bhat
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India.
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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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Ahmad A, Mishra R. Polyol and sugar osmolytes stabilize the molten globule state of α-lactalbumin and inhibit amyloid fibril formation. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140853. [PMID: 36096464 DOI: 10.1016/j.bbapap.2022.140853] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 08/29/2022] [Accepted: 09/02/2022] [Indexed: 06/15/2023]
Abstract
Protein misfolding and aggregation are associated with several human diseases such as Alzheimer's, Parkinson's, prion related disorders, type-II diabetes, etc. Different strategies using molecular chaperones, synthetic and naturally occurring small molecules, osmolytes, etc. have been used to prevent protein aggregation and amyloid fibril formation. In this study, we have used bovine α-lactalbumin at pH 1.6, 37 °C, and shaking conditions to promote amyloid fibril formation. Polyol and sugar osmolytes like glycerol, sorbitol, and trehalose have been used to inhibit the fibrillation of a number of proteins. In the present work, amyloid fibril formation of α-lactalbumin has been shown by ThT assay and AFM, while changes in the secondary structure during fibrillation has been followed by circular dichroism spectroscopy. Our results show that glycerol, sorbitol, and trehalose affect amyloid fibril formation of α-lactalbumin in a concentration-dependent manner. There is a delay in the lag phase of amyloid fibril formation in sorbitol and trehalose and complete inhibition in 6 M glycerol. Our results indicate that delay in the lag phase and inhibition of amyloid fibril formation are due to the stabilization of molten globule state by these osmolytes. At pH 1.6, the molten globule as well as the amyloid fibrils bind to ANS. However, when pH was shifted from 1.6 to 7, only the oligomeric and the fibrillar species bind to ANS due to refolding of molten globule state. The outcome of this study might be useful in designing small molecules which may stabilize the intermediate states, thus preventing amyloid fibril formation.
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Affiliation(s)
- Aziz Ahmad
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Rajesh Mishra
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India.
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Cheah KM, Jun JV, Wittrup KD, Raines RT. Host-Guest Complexation by β-Cyclodextrin Enhances the Solubility of an Esterified Protein. Mol Pharm 2022; 19:3869-3876. [PMID: 36036888 DOI: 10.1021/acs.molpharmaceut.2c00368] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The carboxyl groups of a protein can be esterified by reaction with a diazo compound, 2-diazo-2-(p-methylphenyl)-N,N-dimethylacetamide. This esterification enables the entry of the protein into the cytosol of a mammalian cell, where the nascent ester groups are hydrolyzed by endogenous esterases. The low aqueous solubility of the ensuing esterified protein is, however, a major practical challenge. Solubility screening revealed that β-cyclodextrin (β-CD) is an optimal solubilizing agent for esterified green fluorescent protein (est-GFP). Its addition can increase the recovery of est-GFP by 10-fold. α-CD, γ-CD, and cucurbit-7-uril are less effective excipients. 1H NMR titration experiments revealed that β-CD encapsulates the hydrophobic tolyl group of ester conjugates with Ka = 321 M-1. Combining l-arginine and sucrose with β-CD enables the nearly quantitative recovery of est-GFP. Thus, the insolubility of esterified proteins can be overcome with excipients.
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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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Rodrigues RC, Berenguer-Murcia Á, Carballares D, Morellon-Sterling R, Fernandez-Lafuente R. Stabilization of enzymes via immobilization: Multipoint covalent attachment and other stabilization strategies. Biotechnol Adv 2021; 52:107821. [PMID: 34455028 DOI: 10.1016/j.biotechadv.2021.107821] [Citation(s) in RCA: 222] [Impact Index Per Article: 74.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/26/2021] [Accepted: 08/21/2021] [Indexed: 12/22/2022]
Abstract
The use of enzymes in industrial processes requires the improvement of their features in many instances. Enzyme immobilization, a requirement to facilitate the recovery and reuse of these water-soluble catalysts, is one of the tools that researchers may utilize to improve many of their properties. This review is focused on how enzyme immobilization may improve enzyme stability. Starting from the stabilization effects that an enzyme may experience by the mere fact of being inside a solid particle, we detail other possibilities to stabilize enzymes: generation of favorable enzyme environments, prevention of enzyme subunit dissociation in multimeric enzymes, generation of more stable enzyme conformations, or enzyme rigidification via multipoint covalent attachment. In this last point, we will discuss the features of an "ideal" immobilization protocol to maximize the intensity of the enzyme-support interactions. The most interesting active groups in the support (glutaraldehyde, epoxide, glyoxyl and vinyl sulfone) will be also presented, discussing their main properties and uses. Some instances in which the number of enzyme-support bonds is not directly related to a higher stabilization will be also presented. Finally, the possibility of coupling site-directed mutagenesis or chemical modification to get a more intense multipoint covalent immobilization will be discussed.
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Affiliation(s)
- Rafael C Rodrigues
- Biocatalysis and Enzyme Technology Lab, Institute of Food Science and Technology, Federal University of Rio Grande do Sul, Av. Bento Gonçalves, 9500, P.O. Box 15090, Porto Alegre, RS, Brazil
| | | | - Diego Carballares
- Departamento de Biocatálisis, ICP-CSIC, Campus UAM-CSIC Cantoblanco, Madrid, Spain
| | | | - Roberto Fernandez-Lafuente
- Departamento de Biocatálisis, ICP-CSIC, Campus UAM-CSIC Cantoblanco, Madrid, Spain; Center of Excellence in Bionanoscience Research, External Scientific Advisory Academics, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
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Abstract
Bioelectrocatalysis using redox enzymes appears as a sustainable way for biosensing, electricity production, or biosynthesis of fine products. Despite advances in the knowledge of parameters that drive the efficiency of enzymatic electrocatalysis, the weak stability of bioelectrodes prevents large scale development of bioelectrocatalysis. In this review, starting from the understanding of the parameters that drive protein instability, we will discuss the main strategies available to improve all enzyme stability, including use of chemicals, protein engineering and immobilization. Considering in a second step the additional requirements for use of redox enzymes, we will evaluate how far these general strategies can be applied to bioelectrocatalysis.
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Braham SA, Siar EH, Arana-Peña S, Bavandi H, Carballares D, Morellon-Sterling R, de Andrades D, Kornecki JF, Fernandez-Lafuente R. Positive effect of glycerol on the stability of immobilized enzymes: Is it a universal fact? Process Biochem 2021. [DOI: 10.1016/j.procbio.2020.12.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Sharma GS, Krishna S, Khan S, Dar TA, Khan KA, Singh LR. Protecting thermodynamic stability of protein: The basic paradigm against stress and unfolded protein response by osmolytes. Int J Biol Macromol 2021; 177:229-240. [PMID: 33607142 DOI: 10.1016/j.ijbiomac.2021.02.102] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/12/2021] [Accepted: 02/14/2021] [Indexed: 01/10/2023]
Abstract
Organic osmolytes are known to play important role in stress protection by stabilizing macromolecules and suppressing harmful effects on functional activity. There is existence of several reports in the literature regarding their effects on structural, functional and thermodynamic aspects of many enzymes and the interaction parameters with proteins have been explored. Osmolytes are compatible with enzyme function and therefore, can be accumulated up to several millimolar concentrations. From the thermodynamic point of view, osmolyte raises mid-point of thermal denaturation (Tm) of proteins while having no significant effect on ΔGD° (free energy change at physiological condition). Unfavorable interaction with the peptide backbone due to preferential hydration is the major driving force for folding of unfolded polypeptide in presence of osmolyte. However, the thermodynamic basis of stress protection and origin of compatibility paradigm has been a debatable issue. In the present manuscript, we attempt to elaborate the origin of stress protection and compatibility paradigm of osmolytes based on the effect on thermodynamic stability of proteins. We also infer that protective effects of osmolytes on ΔGD° (of proteins) could also indicate its potential involvement in unfolded protein response and overall stress biology on macromolecular level.
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Affiliation(s)
- Gurumayum Suraj Sharma
- Department of Botany, Bhaskaracharya College of Applied Sciences, University of Delhi, Delhi, India
| | - Snigdha Krishna
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - Sheeza Khan
- School of Life Sciences, B. S. Abdur Rahman Crescent Institute of Science and Technology, Chennai, India
| | - Tanveer A Dar
- Department of Clinical Biochemistry, University of Kashmir, Srinagar, J&K, India
| | - Khurshid A Khan
- School of Life Sciences, B. S. Abdur Rahman Crescent Institute of Science and Technology, Chennai, India
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Arana-Peña S, Rios NS, Carballares D, Gonçalves LR, Fernandez-Lafuente R. Immobilization of lipases via interfacial activation on hydrophobic supports: Production of biocatalysts libraries by altering the immobilization conditions. Catal Today 2021. [DOI: 10.1016/j.cattod.2020.03.059] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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12
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Li J, Chen J, An L, Yuan X, Yao L. Polyol and sugar osmolytes can shorten protein hydrogen bonds to modulate function. Commun Biol 2020; 3:528. [PMID: 32968183 PMCID: PMC7511342 DOI: 10.1038/s42003-020-01260-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 08/28/2020] [Indexed: 12/19/2022] Open
Abstract
Polyol and sugar osmolytes are commonly used in therapeutic protein formulations. How they may affect protein structure and function is an important question. In this work, through NMR measurements, we show that glycerol and sorbitol (polyols), as well as glucose (sugar), can shorten protein backbone hydrogen bonds. The hydrogen bond shortening is also captured by molecular dynamics simulations, which suggest a hydrogen bond competition mechanism. Specifically, osmolytes weaken hydrogen bonds between the protein and solvent to strengthen those within the protein. Although the hydrogen bond change is small, with the average experimental cross hydrogen bond 3hJNC' coupling of two proteins GB3 and TTHA increased by ~ 0.01 Hz by the three osmolytes (160 g/L), its effect on protein function should not be overlooked. This is exemplified by the PDZ3-peptide binding where several intermolecular hydrogen bonds are formed and osmolytes shift the equilibrium towards the bound state.
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Affiliation(s)
- Jingwen Li
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Jingfei Chen
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Liaoyuan An
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoxiang Yuan
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lishan Yao
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
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Insight into the binding of glycerol with myoglobin: Spectroscopic and MD simulation approach. Int J Biol Macromol 2020; 159:433-443. [PMID: 32360459 DOI: 10.1016/j.ijbiomac.2020.04.065] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 04/05/2020] [Accepted: 04/08/2020] [Indexed: 12/18/2022]
Abstract
Stability of proteins plays a significant role not only in their biological function but also in medical science and protein engineering. Since proteins are only stable in special conditions, maintaining their stability and function in biological and biotechnological applications may pose serious challenges. Osmolytes provide a general method of shielding proteins from the unfolding and aggregation caused by extreme stress on the environment. In such studies, the researchers used spectroscopic and simulation approaches to study the alterations of the myoglobin structure and stability in glycerol presence. Experimental results showed a stability improvement of the complex myoglobin-glycerol. After the addition of glycerol resulting in the initiation of hydrogen bonds and higher levels of hydrophobicity, the increase of the Tm was observed. The static mode quenching observed in this study. Van der Waals forces and hydrogen bindings had a decisive and significant role concerning the stability of protein which was consistent with the modeling results. Molecular dynamics simulation showed that the glycerol presence could enhance myoglobin stability. The consistency between the theoretical studies and experimental findings demonstrates that the method proposed in this study could provide a useful method for protein-ligand complex investigations.
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Disorder under stress: Role of polyol osmolytes in modulating fibrillation and aggregation of intrinsically disordered proteins. Biophys Chem 2020; 264:106422. [PMID: 32707418 DOI: 10.1016/j.bpc.2020.106422] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/19/2020] [Accepted: 06/20/2020] [Indexed: 12/18/2022]
Abstract
Intrinsically disordered proteins (IDPs) comprise ~30-40% of the proteome, have key roles in cellular processes, and have been reported to be involved in stress regulation working in synergy with osmolytes. Osmolytes are known to accumulate against various stresses in living systems and are known to stabilize the native conformation of globular proteins. However, little is known of their effect on IDPs and their mechanism of action is unclear. We have investigated the effect of a series of polyol osmolytes on the conformation, aggregation and fibrillation properties of the IDPs α and β-synuclein, involved in Parkinson's disease, using fluorescence, CD, light scattering and TEM. We observe inhibition of fibril and aggregate formation with increasing concentration as well as the number of hydroxyl groups in polyols as observed by light scattering measurements which correlates well with the increase in viscosity of solution with increasing number of OH groups in them. However, ThT assay, while indicating suppression of fibril formation at various concentrations of polyols, shows enhanced fibrillation at some other concentrations which could be due to the heterogeneity of the species formed that are ThT insensitive. Fibril formation was, thus, probed by using Nile red fluorescence which showed sensitivity towards the species formed. ANS binding fluorescence also indicates a decrease in the hydrophobicity of the fibrils with increasing number of OH groups in polyols. Polyols do not have any effect on the fibrillation of β-syn but lead to enhanced amorphous aggregate formation in presence of Ethylene Glycol and Glycerol and a reduction in the presence of Sorbitol. The net free energy of transfer of the proteins from water to Sorbitol is large and positive while it is relatively negligible in the case of Glycerol suggestive of greater preferential exclusion effect of Sorbitol in comparison with Glycerol in the case of IDPs as well. The results overall show differential and complex effect of osmolytes towards the fibrillation/aggregation properties of the two IDPs and suggest that an appropriate balance between the concentration and type of polyol or osmolyte would be required for the survival of organisms rich in IDPs under various stress conditions.
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Arana-Peña S, Rios NS, Carballares D, Mendez-Sanchez C, Lokha Y, Gonçalves LRB, Fernandez-Lafuente R. Effects of Enzyme Loading and Immobilization Conditions on the Catalytic Features of Lipase From Pseudomonas fluorescens Immobilized on Octyl-Agarose Beads. Front Bioeng Biotechnol 2020; 8:36. [PMID: 32181245 PMCID: PMC7059646 DOI: 10.3389/fbioe.2020.00036] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 01/15/2020] [Indexed: 01/28/2023] Open
Abstract
The lipase from Pseudomonas fluorescens (PFL) has been immobilized on octyl-agarose beads under 16 different conditions (varying pH, ionic strength, buffer, adding some additives) at two different loadings, 1 and 60 mg of enzyme/g of support with the objective of check if this can alter the biocatalyst features. The activity of the biocatalysts versus p-nitrophenyl butyrate and triacetin and their thermal stability were studied. The different immobilization conditions produced biocatalysts with very different features. Considering the extreme cases, using 1 mg/g preparations, PFL stability changed more than fourfolds, while their activities versus pNPB or triacetin varied a 50-60%. Curiously, PFL specific activity versus triacetin was higher using highly enzyme loaded biocatalysts than using lowly loaded biocatalysts (even by a twofold factor). Moreover, stability of the highly loaded preparations was higher than that of the lowly loaded preparations, in many instances even when using 5°C higher temperatures (e.g., immobilized in the presence of calcium, the highly loaded biocatalysts maintained after 24 h at 75°c a 85% of the initial activity, while the lowly loaded preparation maintained only 27% at 70°C). Using the highly loaded preparations, activity of the different biocatalysts versus pNPB varied almost 1.7-folds and versus triacetin 1.9-folds. In this instance, the changes in stability caused by the immobilization conditions were much more significant, some preparations were almost fully inactivated under conditions where the most stable one maintained more than 80% of the initial activity. Results suggested that immobilization conditions greatly affected the properties of the immobilized PFL, partially by individual molecule different conformation (observed using lowly loaded preparations) but much more relevantly using highly loaded preparations, very likely by altering some enzyme-enzyme intermolecular interactions. There is not an optimal biocatalyst considering all parameters. That way, preparation of biocatalysts using this support may be a powerful tool to tune enzyme features, if carefully controlled.
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Affiliation(s)
- Sara Arana-Peña
- Departamento de Biocatálisis, Instituto de Catálisis y Petroleoquímica – CSIC, Campus Universidad Autónoma de Madrid – CSIC Cantoblanco, Madrid, Spain
| | - Nathalia S. Rios
- Departamento de Biocatálisis, Instituto de Catálisis y Petroleoquímica – CSIC, Campus Universidad Autónoma de Madrid – CSIC Cantoblanco, Madrid, Spain
- Departamento de Engenharia Química, Universidade Federal do Ceará, Fortaleza, Brazil
| | - Diego Carballares
- Departamento de Biocatálisis, Instituto de Catálisis y Petroleoquímica – CSIC, Campus Universidad Autónoma de Madrid – CSIC Cantoblanco, Madrid, Spain
| | - Carmen Mendez-Sanchez
- Departamento de Biocatálisis, Instituto de Catálisis y Petroleoquímica – CSIC, Campus Universidad Autónoma de Madrid – CSIC Cantoblanco, Madrid, Spain
| | - Yuliya Lokha
- Departamento de Biocatálisis, Instituto de Catálisis y Petroleoquímica – CSIC, Campus Universidad Autónoma de Madrid – CSIC Cantoblanco, Madrid, Spain
| | | | - Roberto Fernandez-Lafuente
- Departamento de Biocatálisis, Instituto de Catálisis y Petroleoquímica – CSIC, Campus Universidad Autónoma de Madrid – CSIC Cantoblanco, Madrid, Spain
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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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17
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Lokha Y, Arana-Peña S, Rios NS, Mendez-Sanchez C, Gonçalves LR, Lopez-Gallego F, Fernandez-Lafuente R. Modulating the properties of the lipase from Thermomyces lanuginosus immobilized on octyl agarose beads by altering the immobilization conditions. Enzyme Microb Technol 2020; 133:109461. [DOI: 10.1016/j.enzmictec.2019.109461] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/29/2019] [Accepted: 11/01/2019] [Indexed: 12/27/2022]
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18
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Fazeli B, Akbari V, Barkhordari A, Mir Mohammad Sadeghi H. Improvement of Soluble Production of Reteplase in Escherichia coli by Optimization of Chemical Chaperones in Lysis Buffer. Adv Biomed Res 2019; 8:65. [PMID: 31737582 PMCID: PMC6839271 DOI: 10.4103/abr.abr_212_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 06/27/2019] [Accepted: 07/09/2019] [Indexed: 11/04/2022] Open
Abstract
Background Reteplase is a nonglycosylated derivative of recombinant tissue plasminogen activator, a thrombolytic agent, which can be easily expressed in Escherichia coli. However, overexpression of reteplase in E. coli usually leads to accumulation of insoluble and inactive aggregates and inclusion bodies. In the present study, we aimed to optimize chemical additives of lysis buffer to avoid the initial aggregation and formation of inclusion bodies of reteplase at cell disruption step. Materials and Methods After protein expression in E. coli BL21 (DE3), the bacterial cells were disrupted in different lysis buffers using microsmashing. Eleven chemical additives at two concentration levels were combined based on a Plackett-Burman design to prepare 12 different lysis buffers used at cell disruption stage. Then, three additives with the most positive effect on improvement of solubility of reteplase were chosen and used for the second screening based on Box-Behnken model. Results The primary screening results showed that among 11 additives, arginine, K2PO4, and cetyltrimethylammonium bromide (CTAB) had the most positive effect on solubility of reteplase. Our final results based on 14 runs of Box-Behnken design showed that the optimum buffer additive condition is 0.005 mg/ml CTAB, 0.065 mg/ml arginine, and 0.026 mg/ml K2PO4. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis and Western blotting of soluble and total fraction of samples confirmed that these additives significantly improved soluble production of reteplase compared with control. Conclusion Our study indicates that the application of chemical additives in cell lysis can improve the solubility of reteplase. Further studies are still required to understand the exact mechanism of chemical additives as a chemical chaperone during cell lysis.
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Affiliation(s)
- Behnaz Fazeli
- Department of Pharmaceutical Biotechnology, Isfahan Pharmaceutical Research Center, Faculty of Pharmacy, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Vajihe Akbari
- Department of Pharmaceutical Biotechnology, Isfahan Pharmaceutical Research Center, Faculty of Pharmacy, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Asgar Barkhordari
- Department of Pharmaceutical Biotechnology, Isfahan Pharmaceutical Research Center, Faculty of Pharmacy, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hamid Mir Mohammad Sadeghi
- Department of Pharmaceutical Biotechnology, Isfahan Pharmaceutical Research Center, Faculty of Pharmacy, Isfahan University of Medical Sciences, Isfahan, Iran
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19
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Dal Magro L, Kornecki JF, Klein MP, Rodrigues RC, Fernandez‐Lafuente R. Stability/activity features of the main enzyme components of rohapect 10L. Biotechnol Prog 2019; 35:e2877. [DOI: 10.1002/btpr.2877] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 05/31/2019] [Accepted: 06/24/2019] [Indexed: 02/06/2023]
Affiliation(s)
- Lucas Dal Magro
- Department of Biocatalysis, ICP‐CSICCampus UAM‐CSIC, Cantoblanco Madrid ZC Spain
- Biotechnology, Bioprocess and Biocatalysis GroupInstitute of Food Science and Technology, Federal University of Rio Grande do Sul Porto Alegre RS Brazil
| | - Jakub F. Kornecki
- Department of Biocatalysis, ICP‐CSICCampus UAM‐CSIC, Cantoblanco Madrid ZC Spain
| | - Manuela P. Klein
- Department of NutritionFederal University of Health Sciences of Porto Alegre (UFCSPA) Porto Alegre RS Brazil
| | - Rafael C. Rodrigues
- Biotechnology, Bioprocess and Biocatalysis GroupInstitute of Food Science and Technology, Federal University of Rio Grande do Sul Porto Alegre RS Brazil
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20
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Libardi N, Soccol CR, Tanobe VOA, Vandenberghe LPDS. Definition of Liquid and Powder Cellulase Formulations Using Domestic Wastewater in Bubble Column Reactor. Appl Biochem Biotechnol 2019; 190:113-128. [PMID: 31301011 DOI: 10.1007/s12010-019-03075-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 07/05/2019] [Indexed: 12/18/2022]
Abstract
Raw domestic wastewater was used as a culture medium for cellulase production in a bubble column reactor (6.2 UFP/mL, 64.6 U/L h) using the strain Trichoderma harzianum TRIC03-LPBII. Cellulases presented optimum pH and temperature between 4 and 5 and 50 and 70 °C, respectively. Enzymatic extract was concentrated through ultrafiltration and then a cellulolytic formulation was prepared with the addition of sorbitol (50% w/v) and benzoic acid (0.05% w/v). High cellulase stability of around 100% was reached after 30 days at 4 °C. The concentrated extract was also dried in a spray-dryer with the addition of maltodextrin at 20% (w/v), resulting in powder enzymatic formulation with 85% stability after 60 days. With these characteristics, the liquid and powder cellulase products have potential to be used in different industrial applications.
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Affiliation(s)
- Nelson Libardi
- Departamento de Engenharia de Bioprocessos e Biotecnologia, Universidade Federal do Paraná-UFPR, Curitiba, PR, 81531-980, Brazil
| | - Carlos Ricardo Soccol
- Departamento de Engenharia de Bioprocessos e Biotecnologia, Universidade Federal do Paraná-UFPR, Curitiba, PR, 81531-980, Brazil
| | - Valcineide O A Tanobe
- Departamento de Engenharia de Bioprocessos e Biotecnologia, Universidade Federal do Paraná-UFPR, Curitiba, PR, 81531-980, Brazil
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21
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Wlodarczyk SR, Costa-Silva TA, Pessoa-Jr A, Madeira P, Monteiro G. Effect of osmolytes on the activity of anti-cancer enzyme L-Asparaginase II from Erwinia chrysanthemi. Process Biochem 2019. [DOI: 10.1016/j.procbio.2019.03.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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22
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Roy S, Bhat R. Effect of polyols on the structure and aggregation of recombinant human γ-Synuclein, an intrinsically disordered protein. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:1029-1042. [DOI: 10.1016/j.bbapap.2018.07.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 06/06/2018] [Accepted: 07/05/2018] [Indexed: 10/28/2022]
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23
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Khoshnevisan G, Emamzadeh R, Nazari M, Rasa SMM, Sariri R, Hassani L. Kinetics, structure, and dynamics of Renilla luciferase solvated in binary mixtures of glycerol and water and the mechanism by which glycerol obstructs the enzyme emitter site. Int J Biol Macromol 2018; 117:617-624. [DOI: 10.1016/j.ijbiomac.2018.05.160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 05/12/2018] [Accepted: 05/22/2018] [Indexed: 11/26/2022]
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24
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Turner MR, Balu-Iyer SV. Challenges and Opportunities for the Subcutaneous Delivery of Therapeutic Proteins. J Pharm Sci 2018; 107:1247-1260. [PMID: 29336981 PMCID: PMC5915922 DOI: 10.1016/j.xphs.2018.01.007] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 12/21/2017] [Accepted: 01/03/2018] [Indexed: 12/22/2022]
Abstract
Biotherapeutics is a rapidly growing drug class, and over 200 biotherapeutics have already obtained approval, with about 50 of these being approved in 2015 and 2016 alone. Several hundred protein therapeutic products are still in the pipeline, including interesting new approaches to treatment. Owing to patients' convenience of at home administration and reduced number of hospital visits as well as the reduction in treatment costs, subcutaneous (SC) administration of biologics is of increasing interest. Although several avenues for treatment using biotherapeutics are being explored, there is still a sufficient gap in knowledge regarding the interplay of formulation conditions, immunogenicity, and pharmacokinetics (PK) of the absorption of these compounds when they are given SC. This review seeks to highlight the major concerns and important factors governing this route of administration and suggest a holistic approach for effective SC delivery.
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Affiliation(s)
- Michael R Turner
- Department of Pharmaceutical Sciences, University at Buffalo, The State University of New York, Buffalo, New York 14214
| | - Sathy V Balu-Iyer
- Department of Pharmaceutical Sciences, University at Buffalo, The State University of New York, Buffalo, New York 14214.
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25
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Roles of osmolytes in protein folding and aggregation in cells and their biotechnological applications. Int J Biol Macromol 2018; 109:483-491. [DOI: 10.1016/j.ijbiomac.2017.12.100] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 12/19/2017] [Indexed: 12/19/2022]
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26
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Efficient osmolyte-based procedure to increase expression level and solubility of infectious hematopoietic necrosis virus (IHNV) nucleoprotein in E. coli. Appl Microbiol Biotechnol 2018; 102:4087-4100. [DOI: 10.1007/s00253-018-8907-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 02/26/2018] [Accepted: 02/28/2018] [Indexed: 01/21/2023]
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27
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Wang G, Bondarenko PV, Kaltashov IA. Multi-step conformational transitions in heat-treated protein therapeutics can be monitored in real time with temperature-controlled electrospray ionization mass spectrometry. Analyst 2018; 143:670-677. [PMID: 29303166 DOI: 10.1039/c7an01655g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Heat-induced conformational transitions are frequently used to probe the free energy landscapes of proteins. However, the extraction of information from thermal denaturation profiles pertaining to non-native protein conformations remains challenging due to their transient nature and significant conformational heterogeneity. Previously we developed a temperature-controlled electrospray ionization (ESI) source that allowed unfolding and association of biopolymers to be monitored by mass spectrometry (MS) in real time as a function of temperature. The scope of this technique is now extended to systems that undergo multi-step denaturation upon heat stress, as well as relatively small-scale conformational changes that are precursors to protein aggregation. The behavior of two therapeutic proteins (human antithrombin and an IgG1 monoclonal antibody) under heat-stress conditions is monitored in real time, providing evidence that relatively small-scale conformational changes in each system lead to protein oligomerization, followed by aggregation. Temperature-controlled ESI MS is particularly useful for the studies of heat-stressed multi-domain proteins such as IgG, where it allows distinct transitions to be observed. The ability of native temperature-controlled ESI MS to monitor both the conformational changes and oligomerization/degradation with high selectivity complements the classic calorimetric methods, lending itself as a powerful experimental tool for the thermostability studies of protein therapeutics.
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Affiliation(s)
- Guanbo Wang
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of Biomedical Materials, and School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, Jiangsu, China.
| | - Pavel V Bondarenko
- Attribute Sciences, Process Development, Amgen, Inc., Thousand Oaks, CA, USA
| | - Igor A Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, USA
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28
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Manning MC, Liu J, Li T, Holcomb RE. Rational Design of Liquid Formulations of Proteins. THERAPEUTIC PROTEINS AND PEPTIDES 2018; 112:1-59. [DOI: 10.1016/bs.apcsb.2018.01.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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29
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Rabbani G. WITHDRAWN: Role of osmolytes in protein folding and aggregation in cells and its applications in biotechnology. Int J Biol Macromol 2017:S0141-8130(17)32827-1. [PMID: 29137994 DOI: 10.1016/j.ijbiomac.2017.11.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/20/2017] [Accepted: 11/06/2017] [Indexed: 11/26/2022]
Abstract
This article has been withdrawn at the request of the author(s) and/or editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at https://www.elsevier.com/about/our-business/policies/article-withdrawal.
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Affiliation(s)
- Gulam Rabbani
- Department of Medical Biotechnology, YeungNam University, 280 Daehak-ro, Gyeongsan, Gyeongbuk, 38541, Republic of Korea.
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30
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Pazhang M, Mardi N, Mehrnejad F, Chaparzadeh N. The combinatorial effects of osmolytes and alcohols on the stability of pyrazinamidase: Methanol affects the enzyme stability through hydrophobic interactions and hydrogen bonds. Int J Biol Macromol 2017; 108:1339-1347. [PMID: 29129628 DOI: 10.1016/j.ijbiomac.2017.11.039] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 11/01/2017] [Accepted: 11/08/2017] [Indexed: 11/24/2022]
Abstract
Inside the cells, proteins are surrounded by mixtures of different osmolytes. However, our current understanding of the combinatorial effects of such mixtures on the stability of proteins remains elusive. In the present study, the stability and structure of recombinant pyrazinamidase (PZase) from Mycobacterium tuberculosis were analyzed in the presence of stabilizing osmolytes (sorbitol, sucrose and glycerol) and alcohols (methanol, ethanol, isopropanol and n-propanol). The far-UV and near-UV circular dichroism (CD), intrinsic fluorescence and thermostability results indicated that methanol, unexpectedly, has stronger effect on destabilization of the enzyme compared to ethanol which has larger log P. Interestingly, the relative half-life of PZase was longer in mixtures methanol with the osmolytes, sorbitol or sucrose (expectedly), or glycerol (unexpectedly), compared to other alcohols. Molecular dynamics simulation results showed that methanol increases the flexibility of region 5-40 and loop 51-71 in the PZase, which are potentially crucial for the stability and activity of the enzyme, respectively. Our results indicated that methanol can interact with PZase via hydrophobic interactions and hydrogen bonds, and therefore resulting in destabilization of the structure of the enzyme. In addition, glycerol probably increases the stability of the enzyme in methanol by disrupting the unfavorable hydrophobic interactions and hydrogen bonds.
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Affiliation(s)
- Mohammad Pazhang
- Department of Cellular and Molecular Biology, Faculty of Science, Azarbaijan Shahid Madani University, Tabriz, Iran.
| | - Narges Mardi
- Department of Cellular and Molecular Biology, Faculty of Science, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Faramarz Mehrnejad
- Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran
| | - Nader Chaparzadeh
- Department of Cellular and Molecular Biology, Faculty of Science, Azarbaijan Shahid Madani University, Tabriz, Iran
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31
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Rashid N, Thapliyal C, Chaudhuri Chattopadhyay P. Osmolyte induced enhancement of expression and solubility of human dihydrofolate reductase: An in vivo study. Int J Biol Macromol 2017; 103:1044-1053. [PMID: 28551440 DOI: 10.1016/j.ijbiomac.2017.05.143] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 05/18/2017] [Accepted: 05/19/2017] [Indexed: 11/18/2022]
Abstract
The process of recombinant protein production in E. coli system is often hampered by the formation of insoluble aggregates. Human Dihydrofolate reductase (hDHFR), an enzyme involved in the synthesis of purine, thymidilate and several other amino acids like glycine, methionine and serine is highly aggregation prone. It catalyzes the reduction of dihydrofolate (H2F) in order to regenerate tetrahydrofolate (H4F) utilizing NADPH as a cofactor. We have attempted to ameliorate the production of soluble and functional protein by growing and inducing the cells under osmotic stress condition, in the presence of various osmolytes like glycerol, sorbitol, TMAO, proline and glycine at 37°C. The expression and yield of functional hDHFR protein were highly enhanced in the presence of these osmolytes. The specific activity of the purified recombinant hDHFR protein has also been increased to a cogent level in the presence of osmolytes. We also observed that protein expressed in presence of the osmolytes was stable in the denaturing conditions as compared to the protein expressed in absence of an osmolyte. We also observed using the intrinsic fluorescence spectroscopy that the osmolytes didn't interfere with the structure of the protein and in denaturing conditions the protein expressed in presence of osmolytes had more stability. Our study is consequential in increasing the production of functional and soluble protein in the cell extract and will also be appropriate to find a therapeutic agent against many neurodegenerative diseases.
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Affiliation(s)
- Naira Rashid
- Amity Institute of Biotechnology, Molecular Biophysics Lab, Amity University, Sector 125, Noida, Uttar Pradesh, 201313, India
| | - Charu Thapliyal
- Kusuma School of Biological Sciences, Indian Institute of Technology, Haus Khas, New Delhi, 110016, India
| | - Pratima Chaudhuri Chattopadhyay
- Amity Institute of Biotechnology, Molecular Biophysics Lab, Amity University, Sector 125, Noida, Uttar Pradesh, 201313, India.
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32
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Zaak H, Siar EH, Kornecki JF, Fernandez-Lopez L, Pedrero SG, Virgen-Ortíz JJ, Fernandez-Lafuente R. Effect of immobilization rate and enzyme crowding on enzyme stability under different conditions. The case of lipase from Thermomyces lanuginosus immobilized on octyl agarose beads. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.02.024] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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33
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Balcão VM, Vila MMDC. Structural and functional stabilization of protein entities: state-of-the-art. Adv Drug Deliv Rev 2015; 93:25-41. [PMID: 25312675 DOI: 10.1016/j.addr.2014.10.005] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 08/03/2014] [Accepted: 10/01/2014] [Indexed: 12/13/2022]
Abstract
Within the context of biomedicine and pharmaceutical sciences, the issue of (therapeutic) protein stabilization assumes particular relevance. Stabilization of protein and protein-like molecules translates into preservation of both structure and functionality during storage and/or targeting, and such stabilization is mostly attained through establishment of a thermodynamic equilibrium with the (micro)environment. The basic thermodynamic principles that govern protein structural transitions and the interactions of the protein molecule with its (micro)environment are, therefore, tackled in a systematic fashion. Highlights are given to the major classes of (bio)therapeutic molecules, viz. enzymes, recombinant proteins, (macro)peptides, (monoclonal) antibodies and bacteriophages. Modification of the microenvironment of the biomolecule via multipoint covalent attachment onto a solid surface followed by hydrophilic polymer co-immobilization, or physical containment within nanocarriers, are some of the (latest) strategies discussed aiming at full structural and functional stabilization of said biomolecules.
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Affiliation(s)
- Victor M Balcão
- LaBNUS - Biomaterials and Nanotechnology Laboratory, i(bs)(2) - intelligent biosensing and biomolecule stabilization research group, University of Sorocaba, Sorocaba, SP, Brazil; CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal.
| | - Marta M D C Vila
- LaBNUS - Biomaterials and Nanotechnology Laboratory, i(bs)(2) - intelligent biosensing and biomolecule stabilization research group, University of Sorocaba, Sorocaba, SP, Brazil
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34
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Kirmair L, Seiler DL, Skerra A. Stability engineering of the Geobacillus stearothermophilus alcohol dehydrogenase and application for the synthesis of a polyamide 12 precursor. Appl Microbiol Biotechnol 2015; 99:10501-13. [PMID: 26329849 DOI: 10.1007/s00253-015-6930-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 08/05/2015] [Accepted: 08/08/2015] [Indexed: 10/23/2022]
Abstract
The thermostable NAD(+)-dependent alcohol dehydrogenase from Geobacillus stearothermophilus (BsADH) was exploited with regard to the biocatalytic synthesis of ω-oxo lauric acid methyl ester (OLAMe), a key intermediate for biobased polyamide 12 production, from the corresponding long-chain alcohol. Recombinant BsADH was produced in Escherichia coli as a homogeneous tetrameric enzyme and showed high activity towards the industrially relevant substrate ω-hydroxy lauric acid methyl ester (HLAMe) with K M = 86 μM and 44 U mg(-1). The equilibrium constant for HLAMe oxidation to the aldehyde (OLAMe) with NAD(+) was determined as 2.16 × 10(-3) from the kinetic parameters of the BsADH-catalyzed forward and reverse reactions. Since BsADH displayed limited stability under oxidizing conditions, the predominant oxidation-prone residue Cys257 was mutated to Leu based on sequence homology with related enzymes and computational simulation. This substitution resulted in an improved BsADH variant exhibiting prolonged stability and an elevated inactivation temperature. Semi-preparative biocatalysis at 60 °C using the stabilized enzyme, employing butyraldehyde for in situ cofactor regeneration with only catalytic amounts of NAD(+), yielded up to 23 % conversion of HLAMe to OLAMe after 30 min. In contrast to other oxidoreductases, no overoxidation to the dodecanoic diacid monomethyl ester was detected. Thus, the mutated BsADH offers a promising biocatalyst for the selective oxidation of fatty alcohols to yield intermediates for industrial polymer production.
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Affiliation(s)
- Ludwig Kirmair
- Munich Center for Integrated Protein Science (CiPSM) and Lehrstuhl für Biologische Chemie, Technische Universität München, 85350, Freising-Weihenstephan, Germany
| | - Daniel Leonard Seiler
- Munich Center for Integrated Protein Science (CiPSM) and Lehrstuhl für Biologische Chemie, Technische Universität München, 85350, Freising-Weihenstephan, Germany
| | - Arne Skerra
- Munich Center for Integrated Protein Science (CiPSM) and Lehrstuhl für Biologische Chemie, Technische Universität München, 85350, Freising-Weihenstephan, Germany.
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35
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Pazhang M, Mehrnejad F, Pazhang Y, Falahati H, Chaparzadeh N. Effect of sorbitol and glycerol on the stability of trypsin and difference between their stabilization effects in the various solvents. Biotechnol Appl Biochem 2015; 63:206-13. [DOI: 10.1002/bab.1366] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 03/05/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Mohammad Pazhang
- Department of Cellular and Molecular Biology; Faculty of Sciences, Azarbaijan Shahid Madani University; Tabriz Iran
| | - Faramarz Mehrnejad
- Department of Life Science Engineering; Faculty of New Sciences & Technologies, University of Tehran; Tehran Iran
| | - Yaghub Pazhang
- Department of Biology; Faculty of Science, Urmia University; Urmia Iran
| | - Hanieh Falahati
- Department of Quantitative and Computational Biology; Princeton University; Princeton NJ USA
| | - Nader Chaparzadeh
- Department of Cellular and Molecular Biology; Faculty of Sciences, Azarbaijan Shahid Madani University; Tabriz Iran
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36
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Boonyuen U, Promnares K, Junkree S, Day NPJ, Imwong M. Efficient in vitro refolding and functional characterization of recombinant human liver carboxylesterase (CES1) expressed in E. coli. Protein Expr Purif 2014; 107:68-75. [PMID: 25462813 PMCID: PMC4294421 DOI: 10.1016/j.pep.2014.11.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 11/10/2014] [Accepted: 11/16/2014] [Indexed: 11/16/2022]
Abstract
Expression of recombinant human carboxylesterase I in E.coli is mainly insoluble. Refolding using a combination of 1% glycerol and 2 mM β-mercaptoethanol in Tris–HCl, pH 7.5 significantly improved solubility. Purified recombinant human CES1 is functionally active and stable. We provided efficient method to produce large amount and catalytically active CES1.
Human liver carboxylesterase 1 (CES1) plays a critical role in the hydrolysis of various ester- and amide-containing molecules, including active metabolites, drugs and prodrugs. However, it has been problematic to express recombinant CES1 in bacterial expression systems due to low solubility, with the CES1 protein being mainly expressed in inclusion bodies, accompanied by insufficient purity issues. In this study, we report an efficient in vitro method for refolding recombinant CES1 from inclusion bodies. A one-step purification with an immobilized-metal affinity column was utilized to purify His-tagged recombinant CES1. Conveniently, both denaturant and imidazole can be removed while the enzyme is refolded via buffer exchange, a dilution method. We show that the refolding of recombinant CES1 was successful in Tris–HCl at pH 7.5 containing a combination of 1% glycerol and 2 mM β-mercaptoethanol, whereas a mixture of other additives (trehalose, sorbitol and sucrose) and β-mercaptoethanol failed to recover a functional protein. His-tagged recombinant CES1 retains its biological activity after refolding and can be used directly without removing the fusion tag. Altogether, our results provide an alternative method for obtaining a substantial amount of functionally active protein, which is advantageous for further investigations such as structural and functional studies.
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Affiliation(s)
- Usa Boonyuen
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand.
| | - Kamoltip Promnares
- Department of Molecular Biotechnology and Bioinformatics, Faculty of Science, Prince of Songkla University, Hat Yai, Songkla 90112, Thailand.
| | - Suwapat Junkree
- Central Equipment Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand.
| | - Nichloas P J Day
- Mahidol Oxford Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; Centre for Tropical Medicine, Nuffield Department of Medicine, Churchill Hospital, Oxford, United Kingdom.
| | - Mallika Imwong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand.
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Pampurova S, Van Dijck P. The desiccation tolerant secrets of Selaginella lepidophylla: what we have learned so far? PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2014; 80:285-90. [PMID: 24813728 DOI: 10.1016/j.plaphy.2014.04.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 04/17/2014] [Indexed: 05/03/2023]
Abstract
Selaginella lepidophylla is a desiccation tolerant plant able to survive complete vegetative tissue dehydration and revive ('resurrect') in water conditions. Vegetative desiccation tolerance is an adaptive feature acquired by S. lepidophylla to withstand the long dry periods in its natural habitat, the Chihuahuan desert. Understanding the molecular basis of its drought stress tolerance may be of great benefit to help in developing novel strategies for improvement of drought stress tolerance in crops. Cell biological (e.g. gene discovery, comparative EST analysis, proteomics, metabolite profiling), ultrastructural and physiological studies have brought modest but already important insights in the desiccation tolerance mechanisms adapted by S. lepidophylla. Until recently, the desiccation tolerant mechanism of S. lepidophylla was related to its high trehalose levels. However, large-scale comparative metabolic analysis between S. lepidophylla and its desiccation susceptible relative Selaginella moellendorffii, unexpectedly revealed that S. moellendorffii contains higher trehalose levels than S. lepidophylla. Interestingly, polyols, such as sorbitol and xylitol are 100× more abundant in S. lepidophylla compared to S. moellendorffii. Whether this is linked to the higher stress tolerance remains to be established. Apart from these metabolites, we will also discuss the ultrastructural features that seem to play an important role in the desiccation tolerance of S. lepidophylla. Finally we discuss desiccation tolerance mechanism in other plant species.
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Affiliation(s)
- Suzana Pampurova
- Department of Molecular Microbiology, VIB, Leuven, Belgium; Laboratory of Molecular Cell Biology, KU Leuven, Kasteelpark Arenberg 31 Bus 2438, 3001 Leuven, Belgium
| | - Patrick Van Dijck
- Department of Molecular Microbiology, VIB, Leuven, Belgium; Laboratory of Molecular Cell Biology, KU Leuven, Kasteelpark Arenberg 31 Bus 2438, 3001 Leuven, Belgium.
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Levy-Sakin M, Berger O, Feibish N, Sharon N, Schnaider L, Shmul G, Amir Y, Buzhansky L, Gazit E. The influence of chemical chaperones on enzymatic activity under thermal and chemical stresses: common features and variation among diverse chemical families. PLoS One 2014; 9:e88541. [PMID: 24520396 PMCID: PMC3919781 DOI: 10.1371/journal.pone.0088541] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 01/06/2014] [Indexed: 11/18/2022] Open
Abstract
Molecular and chemical chaperones are key components of the two main mechanisms that ensure structural stability and activity under environmental stresses. Yet, chemical chaperones are often regarded only as osmolytes and their role beyond osmotic regulation is not fully understood. Here, we systematically studied a large group of chemical chaperones, representatives of diverse chemical families, for their protective influence under either thermal or chemical stresses. Consistent with previous studies, we observed that in spite of the structural similarity between sugars and sugar alcohols, they have an apparent difference in their protective potential. Our results support the notion that the protective activity is mediated by the solvent and the presence of water is essential. In the current work we revealed that i) polyols and sugars have a completely different profile of protective activity toward trifluoroethanol and thermal stress; ii) minor changes in solvent composition that do not affect enzyme activity, yet have a great effect on the ability of osmolytes to act as protectants and iii) increasing the number of active groups of carbohydrates makes them better protectants while increasing the number of active groups of methylamines does not, as revealed by attempts to synthesize de novo designed methylamines with multiple functional groups.
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Affiliation(s)
- Michal Levy-Sakin
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Or Berger
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Nir Feibish
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Noa Sharon
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Lee Schnaider
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Guy Shmul
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Yaniv Amir
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Ludmila Buzhansky
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
- * E-mail:
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Dave AC, Loveday SM, Anema SG, Jameson GB, Singh H. Modulating β-Lactoglobulin Nanofibril Self-Assembly at pH 2 Using Glycerol and Sorbitol. Biomacromolecules 2013; 15:95-103. [DOI: 10.1021/bm401315s] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Anant C. Dave
- Riddet
Institute, Massey University, Private Bag 11 222, Palmerston North, New Zealand
| | - Simon M. Loveday
- Riddet
Institute, Massey University, Private Bag 11 222, Palmerston North, New Zealand
| | - Skelte G. Anema
- Riddet
Institute, Massey University, Private Bag 11 222, Palmerston North, New Zealand
- Fonterra
Research and Development Centre, Private Bag 11 029, Palmerston North, New Zealand
| | - Geoffrey B. Jameson
- Riddet
Institute, Massey University, Private Bag 11 222, Palmerston North, New Zealand
- Institute
of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North, New Zealand
| | - Harjinder Singh
- Riddet
Institute, Massey University, Private Bag 11 222, Palmerston North, New Zealand
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He X, Lopes PEM, MacKerell AD. Polarizable empirical force field for acyclic polyalcohols based on the classical Drude oscillator. Biopolymers 2013; 99:724-38. [PMID: 23703219 PMCID: PMC3902549 DOI: 10.1002/bip.22286] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 05/05/2013] [Indexed: 01/12/2023]
Abstract
A polarizable empirical force field for acyclic polyalcohols based on the classical Drude oscillator is presented. The model is optimized with an emphasis on the transferability of the developed parameters among molecules of different sizes in this series and on the condensed-phase properties validated against experimental data. The importance of the explicit treatment of electronic polarizability in empirical force fields is demonstrated in the cases of this series of molecules with vicinal hydroxyl groups that can form cooperative intra- and intermolecular hydrogen bonds. Compared to the CHARMM additive force field, improved treatment of the electrostatic interactions avoids overestimation of the gas-phase dipole moments resulting in significant improvement in the treatment of the conformational energies and leads to the correct balance of intra- and intermolecular hydrogen bonding of glycerol as evidenced by calculated heat of vaporization being in excellent agreement with experiment. Computed condensed phase data, including crystal lattice parameters and volumes and densities of aqueous solutions are in better agreement with experimental data as compared to the corresponding additive model. Such improvements are anticipated to significantly improve the treatment of polymers in general, including biological macromolecules.
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Affiliation(s)
- Xibing He
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201
| | - Pedro E. M. Lopes
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201
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Zhang N, Liu FF, Dong XY, Sun Y. Counteraction of trehalose on urea-induced protein unfolding: Thermodynamic and kinetic studies. Biochem Eng J 2013. [DOI: 10.1016/j.bej.2013.07.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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42
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Yobi A, Wone BWM, Xu W, Alexander DC, Guo L, Ryals JA, Oliver MJ, Cushman JC. Metabolomic profiling in Selaginella lepidophylla at various hydration states provides new insights into the mechanistic basis of desiccation tolerance. MOLECULAR PLANT 2013; 6:369-85. [PMID: 23239830 DOI: 10.1093/mp/sss155] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Selaginella lepidophylla is one of only a few species of spike mosses (Selaginellaceae) that have evolved desiccation tolerance (DT) or the ability to 'resurrect' from an air-dried state. In order to understand the metabolic basis of DT, S. lepidophylla was subjected to a five-stage, rehydration/dehydration cycle, then analyzed using non-biased, global metabolomics profiling technology based on GC/MS and UHLC/MS/MS(2) platforms. A total of 251 metabolites including 167 named (66.5%) and 84 (33.4%) unnamed compounds were characterized. Only 42 (16.7%) and 74 (29.5%) of compounds showed significantly increased or decreased abundance, respectively, indicating that most compounds were produced constitutively, including highly abundant trehalose, sucrose, and glucose. Several glycolysis/gluconeogenesis and tricarboxylic acid (TCA) cycle intermediates showed increased abundance at 100% relative water content (RWC) and 50% RWC. Vanillate, a potent antioxidant, was also more abundant in the hydrated state. Many different sugar alcohols and sugar acids were more abundant in the hydrated state. These polyols likely decelerate the rate of water loss during the drying process as well as slow water absorption during rehydration, stabilize proteins, and scavenge reactive oxygen species (ROS). In contrast, nitrogen-rich and γ-glutamyl amino acids, citrulline, and nucleotide catabolism products (e.g. allantoin) were more abundant in the dry states, suggesting that these compounds might play important roles in nitrogen remobilization during rehydration or in ROS scavenging. UV-protective compounds such as 3-(3-hydroxyphenyl)propionate, apigenin, and naringenin, were more abundant in the dry states. Most lipids were produced constitutively, with the exception of choline phosphate, which was more abundant in dry states and likely plays a role in membrane hydration and stabilization. In contrast, several polyunsaturated fatty acids were more abundant in the hydrated states, suggesting that these compounds likely help maintain membrane fluidity during dehydration. Lastly, S. lepidophylla contained seven unnamed compounds that displayed twofold or greater abundance in dry or rehydrating states, suggesting that these compounds might play adaptive roles in DT.
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Affiliation(s)
- Abou Yobi
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557-0330, USA
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Liquid Formulations for Long-Term Storage of Monoclonal IgGs. Appl Biochem Biotechnol 2013; 169:1431-48. [DOI: 10.1007/s12010-012-0084-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 12/28/2012] [Indexed: 10/27/2022]
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Leibly DJ, Nguyen TN, Kao LT, Hewitt SN, Barrett LK, Van Voorhis WC. Stabilizing additives added during cell lysis aid in the solubilization of recombinant proteins. PLoS One 2012; 7:e52482. [PMID: 23285060 PMCID: PMC3527557 DOI: 10.1371/journal.pone.0052482] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 11/19/2012] [Indexed: 11/23/2022] Open
Abstract
Insoluble recombinant proteins are a major issue for both structural genomics and enzymology research. Greater than 30% of recombinant proteins expressed in Escherichia coli (E. coli) appear to be insoluble. The prevailing view is that insolubly expressed proteins cannot be easily solubilized, and are usually sequestered into inclusion bodies. However, we hypothesize that small molecules added during the cell lysis stage can yield soluble protein from insoluble protein previously screened without additives or ligands. We present a novel screening method that utilized 144 additive conditions to increase the solubility of recombinant proteins expressed in E. coli. These selected additives are natural ligands, detergents, salts, buffers, and chemicals that have been shown to increase the stability of proteins in vivo. We present the methods used for this additive solubility screen and detailed results for 41 potential drug target recombinant proteins from infectious organisms. Increased solubility was observed for 80% of the recombinant proteins during the primary and secondary screening of lysis with the additives; that is 33 of 41 target proteins had increased solubility compared with no additive controls. Eleven additives (trehalose, glycine betaine, mannitol, L-Arginine, potassium citrate, CuCl2, proline, xylitol, NDSB 201, CTAB and K2PO4) solubilized more than one of the 41 proteins; these additives can be easily screened to increase protein solubility. Large-scale purifications were attempted for 15 of the proteins using the additives identified and eight (40%) were prepared for crystallization trials during the first purification attempt. Thus, this protocol allowed us to recover about a third of seemingly insoluble proteins for crystallography and structure determination. If recombinant proteins are required in smaller quantities or less purity, the final success rate may be even higher.
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Affiliation(s)
- David J. Leibly
- Department of Allergy and Infectious Disease, School of Medicine, University of Washington, Seattle, Washington, United States of America
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, United States of America
| | - Trang Nhu Nguyen
- Department of Allergy and Infectious Disease, School of Medicine, University of Washington, Seattle, Washington, United States of America
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, United States of America
| | - Louis T. Kao
- Department of Allergy and Infectious Disease, School of Medicine, University of Washington, Seattle, Washington, United States of America
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, United States of America
| | - Stephen N. Hewitt
- Department of Allergy and Infectious Disease, School of Medicine, University of Washington, Seattle, Washington, United States of America
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, United States of America
| | - Lynn K. Barrett
- Department of Allergy and Infectious Disease, School of Medicine, University of Washington, Seattle, Washington, United States of America
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, United States of America
| | - Wesley C. Van Voorhis
- Department of Allergy and Infectious Disease, School of Medicine, University of Washington, Seattle, Washington, United States of America
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, United States of America
- * E-mail:
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46
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Jeong SH. Analytical methods and formulation factors to enhance protein stability in solution. Arch Pharm Res 2012; 35:1871-86. [DOI: 10.1007/s12272-012-1103-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 08/29/2012] [Accepted: 09/12/2012] [Indexed: 11/29/2022]
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47
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48
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Yobi A, Wone BWM, Xu W, Alexander DC, Guo L, Ryals JA, Oliver MJ, Cushman JC. Comparative metabolic profiling between desiccation-sensitive and desiccation-tolerant species of Selaginella reveals insights into the resurrection trait. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 72:983-99. [PMID: 23061970 DOI: 10.1111/tpj.12008] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Spike mosses (Selaginellaceae) represent an ancient lineage of vascular plants in which some species have evolved desiccation tolerance (DT). A sister-group contrast to reveal the metabolic basis of DT was conducted between a desiccation-tolerant species, Selaginella lepidophylla, and a desiccation-sensitive species, Selaginella moellendorffii, at 100% relative water content (RWC) and 50% RWC using non-biased, global metabolomics profiling technology, based on GC/MS and UHLC/MS/MS(2) platforms. A total of 301 metabolites, including 170 named (56.5%) and 131 (43.5%) unnamed compounds, were characterized across both species. S. lepidophylla retained significantly higher abundances of sucrose, mono- and polysaccharides, and sugar alcohols than did S. moellendorffii. Aromatic amino acids, the well-known osmoprotectant betaine and flavonoids were also more abundant in S. lepidophylla. Notably, levels of γ-glutamyl amino acid, linked with glutathione metabolism in the detoxification of reactive oxygen species, and with possible nitrogen remobilization following rehydration, were markedly higher in S. lepidophylla. Markers for lipoxygenase activity were also greater in S. lepidophylla, especially at 50% RWC. S. moellendorffii contained more than twice the number of unnamed compounds, with only a slightly greater abundance than in S. lepidophylla. In contrast, S. lepidophylla contained 14 unnamed compounds of fivefold or greater abundance than in S. moellendorffii, suggesting that these compounds might play critical roles in DT. Overall, S. lepidophylla appears poised to tolerate desiccation in a constitutive manner using a wide range of metabolites with some inducible components, whereas S. moellendorffii mounts only limited metabolic responses to dehydration stress.
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Affiliation(s)
- Abou Yobi
- Department of Biochemistry & Molecular Biology, University of Nevada, Reno, NV 89557-0330, USADepartment of Biological Sciences, University of Nevada, Reno, NV 89557-0314, USAMetabolon Inc., 800 Capitola Drive, Suite 1, Durham, NC 27713, USAU.S. Department of Agriculture-Agricultural Research Service, Plant Genetic Research Unit, University of Missouri, Columbia, MO 65211, USA
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49
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Yobi A, Wone BWM, Xu W, Alexander DC, Guo L, Ryals JA, Oliver MJ, Cushman JC. Comparative metabolic profiling between desiccation-sensitive and desiccation-tolerant species of Selaginella reveals insights into the resurrection trait. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012. [PMID: 23061970 DOI: 10.1111/tpj.12008 [epub ahead of print]] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Spike mosses (Selaginellaceae) represent an ancient lineage of vascular plants in which some species have evolved desiccation tolerance (DT). A sister-group contrast to reveal the metabolic basis of DT was conducted between a desiccation-tolerant species, Selaginella lepidophylla, and a desiccation-sensitive species, Selaginella moellendorffii, at 100% relative water content (RWC) and 50% RWC using non-biased, global metabolomics profiling technology, based on GC/MS and UHLC/MS/MS(2) platforms. A total of 301 metabolites, including 170 named (56.5%) and 131 (43.5%) unnamed compounds, were characterized across both species. S. lepidophylla retained significantly higher abundances of sucrose, mono- and polysaccharides, and sugar alcohols than did S. moellendorffii. Aromatic amino acids, the well-known osmoprotectant betaine and flavonoids were also more abundant in S. lepidophylla. Notably, levels of γ-glutamyl amino acid, linked with glutathione metabolism in the detoxification of reactive oxygen species, and with possible nitrogen remobilization following rehydration, were markedly higher in S. lepidophylla. Markers for lipoxygenase activity were also greater in S. lepidophylla, especially at 50% RWC. S. moellendorffii contained more than twice the number of unnamed compounds, with only a slightly greater abundance than in S. lepidophylla. In contrast, S. lepidophylla contained 14 unnamed compounds of fivefold or greater abundance than in S. moellendorffii, suggesting that these compounds might play critical roles in DT. Overall, S. lepidophylla appears poised to tolerate desiccation in a constitutive manner using a wide range of metabolites with some inducible components, whereas S. moellendorffii mounts only limited metabolic responses to dehydration stress.
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Affiliation(s)
- Abou Yobi
- Department of Biochemistry & Molecular Biology, University of Nevada, Reno, NV 89557-0330, USADepartment of Biological Sciences, University of Nevada, Reno, NV 89557-0314, USAMetabolon Inc., 800 Capitola Drive, Suite 1, Durham, NC 27713, USAU.S. Department of Agriculture-Agricultural Research Service, Plant Genetic Research Unit, University of Missouri, Columbia, MO 65211, USA
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50
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Devaraneni PK, Mishra N, Bhat R. Polyol osmolytes stabilize native-like cooperative intermediate state of yeast hexokinase A at low pH. Biochimie 2012; 94:947-52. [DOI: 10.1016/j.biochi.2011.12.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Accepted: 12/13/2011] [Indexed: 11/29/2022]
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